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 I177 R1
|
141 |
27.5 |
996908 |
97.7% |
973979 |
124.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
438,112 |
A→G |
S370G (AGC→GGC) |
thiI → |
tRNA 4‑thiouridine(8) synthase ThiI |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 438,112 | 0 | A | G | 100.0%
| 55.4
/ NA
| 16 | S370G (AGC→GGC) | thiI | tRNA 4‑thiouridine(8) synthase ThiI |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (9/7); total (9/7) |
CAACCTGGCCCGCCAGATTGGCACCGAAGACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCAGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGCCCGAACGACGTGATCCTC > NZ_CP009273/437979‑438237
|
caACCTGGCCCGCCAGATTGGCACCGAAGACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCCGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCAtt > 1:62975/1‑139 (MQ=255)
gCCCGCCAGATTGGCACCGAAGACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGAt > 1:38458/1‑138 (MQ=255)
ttGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGa < 1:48656/105‑1 (MQ=255)
ttGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGa > 2:48656/1‑105 (MQ=255)
gtgtGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGaa > 1:176588/1‑101 (MQ=255)
gtgtGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGaa < 2:176588/101‑1 (MQ=255)
gtgtGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGAc < 1:277624/139‑1 (MQ=255)
tgATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGAcc > 2:211686/1‑137 (MQ=255)
tcCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCAtt < 1:371133/72‑1 (MQ=255)
tcCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCAtt > 2:371133/1‑72 (MQ=255)
aGCAGTTAAATCGAAGACTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAAcc < 2:62975/139‑1 (MQ=255)
gTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTc > 1:345624/1‑138 (MQ=255)
aaTCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATgg > 2:140684/1‑139 (MQ=255)
agaagTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCA‑GAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGCCCGAACGACGTGATCCTc < 1:211686/139‑1 (MQ=255)
cGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGCCCg < 1:51734/118‑1 (MQ=255)
cGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGCCCg > 2:51734/1‑118 (MQ=255)
|
CAACCTGGCCCGCCAGATTGGCACCGAAGACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCAGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGCCCGAACGACGTGATCCTC > NZ_CP009273/437979‑438237
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ 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
GAGCACATCATCAACCTGGCCCGCCAGATTGGCACCGAAGACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCAGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGCCCGAACGACGTGATCCTCGATATCCGTTCTAT > NZ_CP009273/437968‑438251
|
GAGCACATCATCAACCTGGCCCGCCAGATTGGCACCGAAGACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCCGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTC > SRR3722131.63667/1‑151 (MQ=60)
TCATCAACCTGGCCCGCCAGATTGGCACCGAAGACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATA > SRR3722131.38845/1‑150 (MQ=60)
gacggcatacgagatctagtacggtctcgtgggctcggagatgtgtataagagacagGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGT < SRR3722131.375248/94‑1 (MQ=60)
cggagatgtgtataagagacaGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACG < SRR3722131.49159/128‑1 (MQ=60)
GGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTctgtctcttatacacatctccgagccc > SRR3722131.178616/1‑123 (MQ=60)
GGTGTGCTCTCCATAAGCCTGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCTGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAG < SRR3722131.394174/151‑1 (MQ=60)
GGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAG < SRR3722131.280839/151‑1 (MQ=60)
CGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCA > SRR3722131.349500/1‑150 (MQ=60)
ataagagacagGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGCCCGAACGACGTGAT < SRR3722131.52276/140‑1 (MQ=60)
GAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCA‑GAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGCCCGAACGACGTGATCCTCGATATCCGTTC < SRR3722131.214165/151‑1 (MQ=60)
AGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGCCCGAACGACGTGATCCTCGATATCCGTTCTAT > SRR3722131.360449/1‑151 (MQ=60)
|
GAGCACATCATCAACCTGGCCCGCCAGATTGGCACCGAAGACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCAGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGCCCGAACGACGTGATCCTCGATATCCGTTCTAT > NZ_CP009273/437968‑438251
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
