Sample Resequencing Stats
Note: The mutation counts shown below represent unfiltered mutation sets.
| ALE, Flask, Isolate |
Predicted Mutations |
Mean Coverage |
Total Reads |
Percent Mapped |
Mapped Reads |
Average Read Length |
|
A2 F5 I175 R1
|
328 |
64.7 |
2582366 |
96.2% |
2484236 |
120.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
633,831 |
C→T |
A67T (GCT→ACT) |
dsbG ← |
thiol:disulfide interchange protein DsbG |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 633,831 | 0 | C | T | 86.5%
| 97.9
/ 7.4
| 37 | A67T (GCT→ACT) | dsbG | thiol:disulfide interchange protein DsbG |
| Reads supporting (aligned to +/- strand): ref base C (2/3); new base T (11/21); total (13/24) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.74e-01 |
ACCGTCGAGGAGCCAGTGGGATTGTTCCATCCGTTGCCACATTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGCGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGATAACCTTTCATTCCTCCGGGGGCATCGAATGTTTTGATGATTGTAATGCCCTGTTTTTCAATCGCTTTTACT > NZ_CP009273/633700‑633961
|
aCCGTCGAGGAGCCAGTGGGATTGTTCCATCCGTTGCCACATTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCtt < 2:80815/138‑1 (MQ=255)
gaggagCCAGTGGGATTGTTCCATCCGTTGCCACATTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATc < 2:1219732/138‑1 (MQ=255)
gCCAGTGGGATTGTTCCATCCGTTGCCACATTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGCGTGCTTACCATCTGGAGt < 1:296968/139‑1 (MQ=255)
ccAGTGGGATTGTTCCATCCGTTGCCACATTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTc < 2:723901/139‑1 (MQ=255)
gTTCCATCCGTTGCCACATTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGt > 2:706258/1‑139 (MQ=255)
ccATCCGTTGCCACATTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGa < 1:1217880/138‑1 (MQ=255)
tCCGTTGCCACATTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGcc < 2:178231/139‑1 (MQ=255)
cGTTGCCACATTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCa < 1:19304/139‑1 (MQ=255)
cGTTGCCACATTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCa < 2:693167/139‑1 (MQ=255)
cGTTGCCACATTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCa < 1:319227/139‑1 (MQ=255)
cGTTGCCACATTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCa < 1:706258/139‑1 (MQ=255)
tGCCACATTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCtt < 1:409320/104‑1 (MQ=255)
tGCCACATTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCtt > 1:970779/1‑104 (MQ=255)
tGCCACATTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCtt < 2:970779/104‑1 (MQ=255)
tGCCACATTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCtt > 2:409320/1‑104 (MQ=255)
tGCCACATTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCatat > 2:665104/1‑139 (MQ=255)
tGCCACATTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGCGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCatat > 2:56650/1‑139 (MQ=255)
caTTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGa < 2:679234/139‑1 (MQ=255)
gCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGAt < 1:1056866/139‑1 (MQ=255)
cTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGATa < 2:1260072/139‑1 (MQ=255)
tAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGATAACCTTTCa > 2:964568/1‑139 (MQ=255)
tAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGATAACCTTTCa < 2:977817/139‑1 (MQ=255)
tAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGATAACCTTTCa < 1:209284/139‑1 (MQ=255)
tttCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGCGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGATAACCTTTCATTCCTCCgg < 1:56650/138‑1 (MQ=255)
aGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGATAACCTTTCATTCCTCCGGGGGCATCGa < 2:391190/139‑1 (MQ=255)
aCTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGATAACCTTTCATTCCTCCGGGGGCATCGAATGtttt < 2:49558/138‑1 (MQ=255)
cTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGATAACCTTTCATTCCTCCGGGGGCATCGAATGTTTtga > 2:666791/1‑139 (MQ=255)
aGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGATAACCTTTCATTCCTCCGGGGGCATCGAATGTTTtgat < 2:1110907/137‑1 (MQ=255)
aGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGCGTGCTTACCATCTGGAGt > 2:428745/1‑59 (MQ=255)
aGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGCGTGCTTACCATCTGGAGt < 1:428745/59‑1 (MQ=255)
gTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGa > 2:1160599/1‑71 (MQ=255)
gTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGa < 1:1160599/71‑1 (MQ=255)
aaCCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGATAACCTTTCATTCCTCCGGGGGCATCGAATGTTTTGATGATTGTAATGCCCTGTTTTTCAATCGCttt > 2:885377/1‑139 (MQ=255)
aCCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGATAACCTTTCATTCCTCCGGGGGCATCGAATGTTTTGATGATTGTAATGCCCTGTTTTTCAATCGCttt > 2:830586/1‑138 (MQ=255)
aCCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGATAACCTTTCATTCCTCCGGGGGCATCGAATGTTTTGATGATTGTAATGCCCTGTTTTTCAATCGCttt > 1:302514/1‑138 (MQ=255)
cAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGATAACCTTTCATTCCTCCGGGGGCATCGAATGTTTTGATGATTGTAATGCCCTGTTTTTCAATCGCTTTTAc > 2:813494/1‑139 (MQ=255)
agagATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGATAACCTTTCATTCCTCCGGGGGCATCGAATGTTTTGATGATTGTAATGCCCTGTTTTTCAATCGCTTTTACt < 1:666791/139‑1 (MQ=255)
|
ACCGTCGAGGAGCCAGTGGGATTGTTCCATCCGTTGCCACATTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGCGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGATAACCTTTCATTCCTCCGGGGGCATCGAATGTTTTGATGATTGTAATGCCCTGTTTTTCAATCGCTTTTACT > NZ_CP009273/633700‑633961
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GCATCTTTTTTACCGTCGAGGAGCCAGTGGGATTGTTCCATCCGTTGCCACATTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGCGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGATAACCTTTCATTCCTCCGGGGGCATCGAATGTTTTGATGATTGTAATGCCCTGTTTTTCAATCGCTTTTACTGGAGCAGGAAGTT > NZ_CP009273/633689‑633974
|
GCATCTTTTTTACCGTCGAGGAGCCAGTGGGATTGTTCCATCCGTTGCCACATTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTAC < SRR3722129.900043/151‑1 (MQ=60)
CATCTTTTTTACCGTCGAGGAGCCAGTGGGATTGTTCCATCCGTTGCCACATTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACC < SRR3722129.826346/151‑1 (MQ=60)
gctcggagatgtgtataagagacagGTTCCATCCGTTGCCACATTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAG < SRR3722129.415251/126‑1 (MQ=60)
AGCCAGTGGGATTGTTCCATCCGTTGCCACATTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGCGTGCTTACCATCTGGAGTCAGGTAGATGG < SRR3722129.301217/151‑1 (MQ=60)
tttcaagcagaagacggcatacgagattcgccttagtctcgtgggctcggagatgtgtataagagacagGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGCGTGCTTACCATCTGGAGTCAGGTAGATGG < SRR3722129.434974/81‑1 (MQ=60)
GTTCCATCCGTTGCCACATTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGctgtctcttatacacatctccgagc > SRR3722129.984514/1‑126 (MQ=60)
agacggcatacgagattcgccttagtctcgtgggctcggagatgtgtataagagacagGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCC < SRR3722129.1176780/93‑1 (MQ=60)
TCCATCCGTTGCCACATTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCC < SRR3722129.1234841/150‑1 (MQ=60)
CCGTTGCCACATTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATAC < SRR3722129.323784/151‑1 (MQ=60)
CCGTTGCCACATTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATAC < SRR3722129.716653/151‑1 (MQ=60)
CCGTTGCCACATTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATAC < SRR3722129.19540/151‑1 (MQ=60)
GGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGATAACCTTTCATT < SRR3722129.1071722/151‑1 (MQ=60)
GTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGATAACCTTTCATTCCTCCGGGG < SRR3722129.212195/151‑1 (MQ=60)
TTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGCGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGATAACCTTTCATTCCTCCGGGGGCATCGAAT < SRR3722129.57394/150‑1 (MQ=60)
cgccttagtctcgtgggctcggagatgtgtataagagacagAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGATAACCTTTCATTCCTCCGGGGGCATCGAATGTTTTGATG < SRR3722129.1224652/110‑1 (MQ=60)
TTGTACATGTAACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGATAACCTTTCATTCCTCCGGGGGCATCGAATGTTTTGATGATTGTAATGCCCTGTTTTTCAATCGCTTTT > SRR3722129.306840/1‑150 (MQ=60)
ACCAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGATAACCTTTCATTCCTCCGGGGGCATCGAATGTTTTGATGATTGTAATGCCCTGTTTTTCAATCGCTTTTACTGGAGCAGG > SRR3722129.1089682/1‑150 (MQ=60)
CAGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGATAACCTTTCATTCCTCCGGGGGCATCGAATGTTTTGATGATTGTAATGCCCTGTTTTTCAATCGCTTTTACTGGAGCAGGAAG < SRR3722129.676667/151‑1 (MQ=60)
AGAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGATAACCTTTCATTCCTCCGGGGGCATCGAATGTTTTGATGATTGTAATGCCCTGTTTTTCAATCGCTTTTACTGGAGCAGGAAGT > SRR3722129.68195/1‑151 (MQ=60)
GAGATAGTGTGCTTACCATCTGGAGTCAGGTAGATctgtctcttatacacatctccgagcccacgagactaaggcgaatctcgtatgccgtcttctgcttgaaaaaaaaaaaacaaccacgcaacaacagacagcaacagatcccctagtg > SRR3722129.240659/1‑35 (MQ=59)
|
GCATCTTTTTTACCGTCGAGGAGCCAGTGGGATTGTTCCATCCGTTGCCACATTTCGCGTCCGGCTGGTGCGTAAATTTCTTTTTCGATAAGTGTGTTACTCAGGTTTTCACCTTTCTCGTTGTACATGTAACCAGAGATAGCGTGCTTACCATCTGGAGTCAGGTAGATGGTGACGCCCATATCCTGATACTTTCCGAGATAACCTTTCATTCCTCCGGGGGCATCGAATGTTTTGATGATTGTAATGCCCTGTTTTTCAATCGCTTTTACTGGAGCAGGAAGTT > NZ_CP009273/633689‑633974
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
