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 |
|
A1 F2 I199 R1
|
220 |
57.5 |
3163680 |
97.0% |
3068769 |
86.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,838,813 |
T→C |
I106V (ATT→GTT) |
ynjI ← |
DUF1266 domain‑containing protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,838,813 | 0 | T | C | 97.9%
| 156.1
/ NA
| 48 | I106V (ATT→GTT) | ynjI | DUF1266 domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); major base C (29/18); minor base A (1/0); total (30/18) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CAGCGTTTCAGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAATACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTAATAGAT > NZ_CP009273/1838727‑1838896
|
cAGCGTTTCAGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACAcc > 1:234138/1‑90 (MQ=255)
gTTTCAGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTa > 1:1226023/1‑90 (MQ=255)
gTTTCAGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTa < 2:1352649/90‑1 (MQ=255)
ttCAGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGc < 1:597227/90‑1 (MQ=255)
tCAGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGcc > 2:1207938/1‑90 (MQ=255)
aGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTg < 2:558181/90‑1 (MQ=255)
aGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTg < 2:56446/90‑1 (MQ=255)
aCCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGat < 2:896080/90‑1 (MQ=255)
ttGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGataata > 2:897860/1‑90 (MQ=255)
aTAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGGTACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAgttg > 2:22529/1‑90 (MQ=255)
tAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAgttgt > 1:1513584/1‑90 (MQ=255)
gAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTc > 1:618758/1‑90 (MQ=255)
gAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTc > 1:1265085/1‑90 (MQ=255)
gAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTc > 2:615281/1‑90 (MQ=255)
gATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGata < 1:455497/70‑1 (MQ=255)
gATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGata > 2:455497/1‑70 (MQ=255)
gATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCttttt > 1:2208/1‑90 (MQ=255)
gATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCttttt > 1:940148/1‑90 (MQ=255)
tAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCttttttt > 2:1046336/1‑90 (MQ=255)
tAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCttttttt < 2:327569/90‑1 (MQ=255)
gCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTa > 2:143789/1‑90 (MQ=255)
aGCGCCTGTAACTTCTCGATACTGAGCGGGTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGa > 1:1454078/1‑90 (MQ=255)
aGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGa > 2:212943/1‑90 (MQ=255)
aGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGa < 2:497948/90‑1 (MQ=255)
aGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGa < 2:470829/90‑1 (MQ=255)
aGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGa < 2:321855/90‑1 (MQ=255)
gcgcCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGaa > 2:849494/1‑90 (MQ=255)
cgcCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAAc < 2:231599/90‑1 (MQ=255)
gcCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTg < 2:254954/44‑1 (MQ=255)
gcCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTg > 1:254954/1‑44 (MQ=255)
gcCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACa > 1:243852/1‑90 (MQ=255)
gcCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACa > 2:570516/1‑90 (MQ=255)
cTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAAt > 2:1278969/1‑90 (MQ=255)
cTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAAt > 1:446549/1‑90 (MQ=255)
gTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATaa < 2:1303839/90‑1 (MQ=255)
aaCTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGc < 2:1243355/90‑1 (MQ=255)
cTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGccc < 1:703989/90‑1 (MQ=255)
ctcGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCcat > 2:1529326/1‑90 (MQ=255)
ctcGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCcat < 1:85938/90‑1 (MQ=255)
tcGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCcatc < 1:904895/90‑1 (MQ=255)
cTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCAtaatt > 1:1076778/1‑90 (MQ=255)
gAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCAtaattaa > 2:291405/1‑90 (MQ=255)
gAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCAtaattaa > 2:1373054/1‑90 (MQ=255)
gAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCAtaattaa > 1:1338266/1‑90 (MQ=255)
gAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCAtaattaa > 2:995342/1‑90 (MQ=255)
gAGCGGCTCAAAACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCGCCATCttaattaa > 1:1572009/1‑90 (MQ=255)
aGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCAtaattaat < 1:1428385/90‑1 (MQ=255)
gCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTAATAGAt > 1:1456804/1‑90 (MQ=255)
|
CAGCGTTTCAGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAATACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTAATAGAT > NZ_CP009273/1838727‑1838896
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GCCAGAACTCCAGCGTTTCAGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAATACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTAATAGATAAAGAA > NZ_CP009273/1838717‑1838902
|
GCCAGAACTCCAGCGTTTCAGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACC > SRR3722078.236991/1‑100 (MQ=60)
GAACTCCAGCGTTTCAGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTA > SRR3722078.1245335/1‑100 (MQ=60)
CTCCAGCGTTTCAGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCC < SRR3722078.118275/100‑1 (MQ=60)
TTCAGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAA < SRR3722078.604149/100‑1 (MQ=60)
agagacagGCTTATGAAAGAATCGATAAGGTGCGAACAATTGTAGCGCCTGTAACTCCTCGATACTTAGCGGCTAAACACCTTTAGCTTGATAATAATGC < SRR3722078.683716/92‑1 (MQ=60)
taagagacagTGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGT < SRR3722078.460940/90‑1 (MQ=60)
TTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGT > SRR3722078.1538270/1‑100 (MQ=60)
GCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTC > SRR3722078.625889/1‑100 (MQ=60)
GCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTC > SRR3722078.1285157/1‑100 (MQ=60)
TGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTT > SRR3722078.953201/1‑100 (MQ=60)
TGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTT > SRR3722078.2225/1‑100 (MQ=60)
GATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGGTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGA > SRR3722078.1477786/1‑100 (MQ=60)
CAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCctgtctcttatacacatctgacgctgccgacgatgg > SRR3722078.258078/1‑64 (MQ=60)
CAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACA > SRR3722078.246837/1‑100 (MQ=60)
ATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAAT > SRR3722078.451891/1‑100 (MQ=60)
CTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATT > SRR3722078.1093051/1‑100 (MQ=60)
CTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATT < SRR3722078.712493/100‑1 (MQ=60)
TCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTAA > SRR3722078.1359716/1‑100 (MQ=60)
TCTCGATACTGAGCGGCTCAAAACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCGCCATCTTAATTAA > SRR3722078.1597592/1‑100 (MQ=60)
CTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTAAT < SRR3722078.86949/100‑1 (MQ=60)
TCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTAATA < SRR3722078.917043/100‑1 (MQ=60)
ATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTAATAGAT > SRR3722078.1480554/1‑100 (MQ=60)
AGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTAATAGATAAAGAA < SRR3722078.1451609/100‑1 (MQ=60)
|
GCCAGAACTCCAGCGTTTCAGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAATACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTAATAGATAAAGAA > NZ_CP009273/1838717‑1838902
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
