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 F3 I96 R1
|
172 |
34.7 |
2005794 |
96.2% |
1929573 |
85.4 |
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 | 100.0%
| 161.2
/ NA
| 47 | I106V (ATT→GTT) | ynjI | DUF1266 domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (26/21); total (26/21) |
GTTTCAGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAATACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTAATAGATAA > NZ_CP009273/1838731‑1838898
|
gTTTCAGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTa < 1:362713/90‑1 (MQ=255)
ttCAGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGc < 2:66585/90‑1 (MQ=255)
tCAGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGcc < 2:387513/90‑1 (MQ=255)
aGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTg < 2:619482/90‑1 (MQ=255)
aGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTg < 1:749123/90‑1 (MQ=255)
aTTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGcc > 2:956774/1‑83 (MQ=255)
aTTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGcc < 1:956774/83‑1 (MQ=255)
ttGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGataata > 2:225816/1‑90 (MQ=255)
ttGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGataata > 1:83164/1‑90 (MQ=255)
ttGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGataata > 1:779946/1‑90 (MQ=255)
tATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCa > 2:177145/1‑90 (MQ=255)
gATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGataat > 2:652816/1‑81 (MQ=255)
gATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGataat < 1:652816/81‑1 (MQ=255)
gAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTc > 2:501312/1‑90 (MQ=255)
gttAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCttttt > 2:14676/3‑90 (MQ=255)
tAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCttttttt < 1:100421/90‑1 (MQ=255)
tAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCttttttt < 2:780368/90‑1 (MQ=255)
aGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTg < 1:713336/63‑1 (MQ=255)
aGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTg > 2:713336/1‑63 (MQ=255)
tGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCttt > 1:828109/1‑90 (MQ=255)
gATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTaaa > 1:470649/1‑90 (MQ=255)
gATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTaaa > 1:329639/1‑90 (MQ=255)
aGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGa < 1:666807/90‑1 (MQ=255)
aGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGa < 2:779946/90‑1 (MQ=255)
gcgcCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGaa > 1:782470/1‑90 (MQ=255)
cTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTg < 1:295280/42‑1 (MQ=255)
cTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTg > 2:295280/1‑42 (MQ=255)
tGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATa > 1:704259/1‑90 (MQ=255)
cTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGccc < 2:438838/90‑1 (MQ=255)
tctcGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCca > 2:910982/1‑90 (MQ=255)
ctcGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCcat < 2:329639/90‑1 (MQ=255)
ctcGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCcat < 2:701417/90‑1 (MQ=255)
gAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCAtaattaa > 1:101003/1‑90 (MQ=255)
gAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCAtaattaa > 1:429062/1‑90 (MQ=255)
gAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCAtaattaa > 2:699579/1‑90 (MQ=255)
gAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTT‑AAACCGGcc > 2:490424/1‑63 (MQ=255)
gAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTT‑AAACCGGcc < 1:490424/63‑1 (MQ=255)
ggCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTAATAGa < 2:41877/90‑1 (MQ=255)
ggCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTAATAGa < 1:568887/90‑1 (MQ=255)
gCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGa < 2:146899/62‑1 (MQ=255)
gCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGa > 1:146899/1‑62 (MQ=255)
gCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTAATAGAt > 1:74439/1‑90 (MQ=255)
gCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTAATAGAt > 1:123027/1‑90 (MQ=255)
gCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTAATAGAt > 2:534224/1‑90 (MQ=255)
gCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTAATAGAt > 2:292355/1‑90 (MQ=255)
gCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTAATAGAt > 2:227305/1‑90 (MQ=255)
tCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTAATAGATaa < 1:399361/90‑1 (MQ=255)
|
GTTTCAGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAATACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTAATAGATAA > NZ_CP009273/1838731‑1838898
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GGCCAGAACTCCAGCGTTTCAGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAATACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTAATAGATAAAGAAAAGAGC > NZ_CP009273/1838716‑1838908
|
tcgtcggcagcgtcagatgtgtataagagacagTGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACAC < SRR3722236.961714/67‑1 (MQ=60)
GCCAGAACTCCAGCGTTTCAGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACC < SRR3722236.609211/100‑1 (MQ=60)
CTCCAGCGTTTCAGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCC < SRR3722236.695/100‑1 (MQ=60)
TCCAGCGTTTCAGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCT < SRR3722236.254241/100‑1 (MQ=60)
GTTTCAGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAAT < SRR3722236.367834/100‑1 (MQ=60)
TTTCAGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATA > SRR3722236.84322/1‑100 (MQ=60)
TTTCAGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATA > SRR3722236.793396/1‑100 (MQ=60)
TCAGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAAT < SRR3722236.973651/100‑1 (MQ=60)
atgtgtataagagacagAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGC < SRR3722236.725409/83‑1 (MQ=60)
agccttcgtcggcagcgtcagatgtgtataagagacagATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGC < SRR3722236.299552/62‑1 (MQ=60)
AGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGC < SRR3722236.761960/100‑1 (MQ=60)
ATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTG < SRR3722236.663609/100‑1 (MQ=60)
ATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTT > SRR3722236.842553/1‑100 (MQ=60)
GATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAA > SRR3722236.477624/1‑100 (MQ=60)
GATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAA > SRR3722236.334351/1‑100 (MQ=60)
TAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAAC < SRR3722236.101820/100‑1 (MQ=60)
ATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAA > SRR3722236.795968/1‑100 (MQ=60)
atgtgtataagagacagTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTT‑AAACCGGCCCGAACAATAA < SRR3722236.497807/83‑1 (MQ=60)
TTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATA > SRR3722236.716178/1‑100 (MQ=60)
AGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCC < SRR3722236.677896/100‑1 (MQ=60)
TCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTAA > SRR3722236.102410/1‑100 (MQ=60)
TCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTAA > SRR3722236.435046/1‑100 (MQ=60)
ATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCtgtctcttatacacatc > SRR3722236.149032/1‑83 (MQ=60)
ATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTAATAGAT > SRR3722236.75489/1‑100 (MQ=60)
ATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTAATAGAT > SRR3722236.124761/1‑100 (MQ=60)
GGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTAATAGATAAAGAAAAG < SRR3722236.577647/100‑1 (MQ=60)
TCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTAATAGATAAAGAAAAGAGC < SRR3722236.404940/100‑1 (MQ=60)
|
GGCCAGAACTCCAGCGTTTCAGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAATACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTAATAGATAAAGAAAAGAGC > NZ_CP009273/1838716‑1838908
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
