Re: [wgs-assembler-users] Question on cgw.out output

[Walenz, B. <bw...@jc...>]

Hi, Geoff-  (yes, behind on email)

It’s the distance from the end of the first scaffold to the start of the second one.  The “BA_AB” label means the first scaffold is reversed and the second one is forward.  However, I’m not exactly sure where the distance is measured from.  I would guess it is the lowest coord of each scaffold (X&Y below) but it could also be from 3’ to 3’.

1810018bp from X to Y   X<----------
Y------------------------------------------------------------->

b



On 10/25/13 5:03 PM, "Waldbieser, Geoff" <Geo...@AR...> wrote:

Is the number that follows “gap” the starting position of the insertion?

geoff@RAMbo:/mnt/data2/CocoAssembly14/CA_22/7-0-CGW> grep -B 7 "succeeded with contig" cgw.out | grep "Merge scaffolds" | tail -25
isQualityScaffoldMergingEdge()-- Merge scaffolds 27265 (2959.0bp) and 275496 (19181214.0bp): gap -1810018.9bp +- 6704.2bp weight 3 BA_AB edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 255057 (3728.1bp) and 275505 (19534418.0bp): gap -240550.0bp +- 1503.4bp weight 10 BA_BA edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 196645 (1065.0bp) and 275509 (19566468.0bp): gap -387971.0bp +- 2792.1bp weight 6 BA_AB edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 102999 (8904.9bp) and 275523 (19753393.0bp): gap -3177567.2bp +- 14899.6bp weight 4 AB_AB edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 3002 (14059.2bp) and 275530 (19941091.0bp): gap -36176.4bp +- 1436.3bp weight 10 AB_BA edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 130728 (2557.0bp) and 275532 (19963021.0bp): gap -24261.5bp +- 556.5bp weight 5 AB_BA edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 158301 (1467.0bp) and 275543 (20459003.0bp): gap -341483.1bp +- 6817.8bp weight 4 BA_AB edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 2578 (5620.0bp) and 275544 (20459880.0bp): gap -230824.4bp +- 7767.5bp weight 3 AB_AB edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 256757 (6270.1bp) and 275545 (20459880.0bp): gap -441446.8bp +- 7892.5bp weight 3 AB_AB edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 256706 (7152.3bp) and 275546 (20462065.0bp): gap -597985.2bp +- 9782.8bp weight 3 BA_AB edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 169859 (3338.0bp) and 275554 (20926019.0bp): gap -7353996.3bp +- 87666.8bp weight 7 AB_AB edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 89363 (2520.0bp) and 275565 (21528144.0bp): gap -530220.7bp +- 2990.5bp weight 4 AB_AB edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 137605 (3648.0bp) and 275571 (21574644.0bp): gap -19179.3bp +- 598.9bp weight 5 AB_BA edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 97209 (2991.0bp) and 275574 (21595403.0bp): gap -1329484.3bp +- 6888.5bp weight 5 BA_AB edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 108832 (3143.0bp) and 275575 (21595403.0bp): gap -1364466.4bp +- 8103.7bp weight 4 AB_AB edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 200330 (3653.0bp) and 275590 (22015373.0bp): gap -8198259.3bp +- 26024.1bp weight 4 BA_AB edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 118137 (1070.0bp) and 275598 (22146361.0bp): gap -34650.2bp +- 747.7bp weight 3 AB_BA edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 120336 (3509.0bp) and 275606 (22278336.0bp): gap -1465814.6bp +- 9960.3bp weight 3 BA_AB edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 44863 (1703.0bp) and 275607 (22280305.0bp): gap -1532787.1bp +- 10803.6bp weight 3 AB_AB edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 164622 (3629.0bp) and 275617 (22369299.0bp): gap -4778854.5bp +- 22817.0bp weight 3 BA_AB edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 171746 (2227.0bp) and 275618 (22369299.0bp): gap -4970596.8bp +- 23553.5bp weight 3 BA_AB edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 28139 (7112.0bp) and 275627 (22457141.0bp): gap -5279352.4bp +- 119327.0bp weight 3 AB_AB edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 115015 (2847.0bp) and 275629 (22595843.0bp): gap -161127.7bp +- 960.9bp weight 3 BA_BA edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 46804 (2414.0bp) and 275631 (22596305.0bp): gap -5717371.5bp +- 21776.5bp weight 4 AB_AB edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 140594 (1492.0bp) and 275642 (23025717.0bp): gap -338964.9bp +- 3568.5bp weight 5 BA_AB edge

geoff@RAMbo:/mnt/data2/CocoAssembly14/CA_22/7-0-CGW> grep -B 7 "succeeded without contig" cgw.out | grep "Merge scaffolds" | tail -25
isQualityScaffoldMergingEdge()-- Merge scaffolds 43484 (1256.0bp) and 275616 (22369299.0bp): gap -3811285.9bp +- 17646.8bp weight 3 AB_AB edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 176207 (3169.0bp) and 275619 (22370140.0bp): gap -4992237.9bp +- 24006.4bp weight 3 BA_AB edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 76046 (1455.0bp) and 275620 (22372478.0bp): gap -5025563.5bp +- 117961.1bp weight 3 AB_BA edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 212452 (22404.6bp) and 275621 (22373963.0bp): gap -5198434.2bp +- 24639.0bp weight 3 AB_BA edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 256082 (13669.5bp) and 275622 (22395222.0bp): gap -5186521.9bp +- 19084.6bp weight 5 AB_AB edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 82929 (1082.0bp) and 275623 (22408941.0bp): gap -20478.6bp +- 600.3bp weight 4 BA_BA edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 234338 (27822.9bp) and 275624 (22408941.0bp): gap -956218.7bp +- 6173.5bp weight 3 AB_AB edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 102168 (2679.0bp) and 275625 (22436045.0bp): gap -943548.1bp +- 6082.3bp weight 4 BA_AB edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 210059 (18375.0bp) and 275626 (22438695.0bp): gap -2391622.3bp +- 16237.1bp weight 3 AB_AB edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 242702 (133674.2bp) and 275628 (22461991.0bp): gap -5413283.2bp +- 119246.5bp weight 3 AB_AB edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 137172 (1025.0bp) and 275630 (22595843.0bp): gap -5720434.4bp +- 25165.8bp weight 3 BA_AB edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 194041 (7341.0bp) and 275632 (22596442.0bp): gap -5734829.0bp +- 25228.1bp weight 3 AB_AB edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 95031 (5580.0bp) and 275633 (22603472.0bp): gap -5739511.9bp +- 16512.3bp weight 7 BA_AB edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 265235 (309343.0bp) and 275634 (22608821.0bp): gap -5756824.1bp +- 125387.5bp weight 3 BA_BA edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 265845 (44614.9bp) and 275635 (22918214.0bp): gap -11455756.5bp +- 67995.9bp weight 18 BA_AB edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 222439 (7760.0bp) and 275636 (22964158.0bp): gap -447388.3bp +- 1642.9bp weight 17 AB_BA edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 219987 (30740.0bp) and 275637 (22971968.0bp): gap -313590.7bp +- 2132.8bp weight 10 BA_AB edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 259391 (20621.3bp) and 275638 (22983007.0bp): gap -336934.6bp +- 2791.4bp weight 9 BA_AB edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 182966 (11936.0bp) and 275639 (23003678.0bp): gap -342229.5bp +- 1436.1bp weight 14 AB_BA edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 153932 (6252.0bp) and 275640 (23015419.0bp): gap -366394.0bp +- 2033.3bp weight 7 AB_AB edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 91518 (5186.0bp) and 275641 (23020693.0bp): gap -484056.8bp +- 3462.7bp weight 6 AB_BA edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 198374 (4460.0bp) and 275643 (23025717.0bp): gap -75374.2bp +- 1180.4bp weight 3 AB_BA edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 106339 (4893.0bp) and 275644 (23029023.0bp): gap -271853.9bp +- 2949.4bp weight 3 AB_AB edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 27128 (2895.0bp) and 275645 (23033445.0bp): gap -1152943.7bp +- 7915.6bp weight 3 AB_AB edge
isQualityScaffoldMergingEdge()-- Merge scaffolds 182153 (5442.0bp) and 275646 (23035173.0bp): gap -1688141.4bp +- 9892.4bp weight 3 BA_AB edge


Thanks.
Geoff




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