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 I178 R1
|
167 |
28.0 |
1137820 |
95.3% |
1084342 |
115.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
923,620 |
A→G |
V344V (GTT→GTC) |
cydC ← |
cysteine/glutathione ABC transporter ATP‑binding protein/permease CydC |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 923,620 | 0 | A | G | 100.0%
| 41.7
/ NA
| 12 | V344V (GTT→GTC) | cydC | cysteine/glutathione ABC transporter ATP‑binding protein/permease CydC |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (3/9); total (3/9) |
GTGTTGATTTGCCGCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGAACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCAGAGATACGTACGGCAGAGGCAATGACTTGCCCCAGATGCTGAAATGC > NZ_CP009273/923508‑923754
|
gtgtTGATTTGCCGCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAAcgcg < 1:35123/139‑1 (MQ=255)
gtTGATTTGCCGCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGCTAAGTGAACTGGACATCCCGTAACGTCAGCGAAAAGCGAt > 1:166401/1‑139 (MQ=255)
ttCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGt < 2:351892/139‑1 (MQ=255)
gCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTAt < 1:415200/138‑1 (MQ=255)
aaTCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAg < 2:117930/139‑1 (MQ=255)
tACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGt < 2:4354/138‑1 (MQ=255)
aCCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCTGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGTTGACCTCCGGGTTTTGATCCGtt < 2:564620/138‑1 (MQ=255)
agaAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCagag < 1:295995/139‑1 (MQ=255)
aTCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTcc > 1:430141/1‑111 (MQ=255)
aTCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTcc < 2:430141/111‑1 (MQ=255)
aGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCAGAGATACGTACGGCa < 2:414306/138‑1 (MQ=255)
ccTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCAGAGATACGTACGGCAGAgg > 2:439497/1‑138 (MQ=255)
actggacATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCAGAGATACGTACGGCAGAGGCAATGACTTGCCCCAGATGCTGAAATGc < 1:439497/139‑1 (MQ=255)
|
GTGTTGATTTGCCGCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGAACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCAGAGATACGTACGGCAGAGGCAATGACTTGCCCCAGATGCTGAAATGC > NZ_CP009273/923508‑923754
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ 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
GTTGCGGGTCCCATGCGCGGGTCAGCTGTTGTAACAGTGTTGATTTGCCGCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGAACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCAGAGATACGTACGGCAGAGGCAATGACTTGCCCCAGATGCTGAAATGCACCCGTTACTG > NZ_CP009273/923472‑923765
|
gggctcggagatgtgtataagagacagGTTGTAACAGTGTTGATTTGCCGCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGAC < SRR3722132.471234/124‑1 (MQ=60)
CGGGTCCCATGCGCGGGTCAGCTGTTGTAACAGTGTTGATTTGCCGCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCC < SRR3722132.312553/151‑1 (MQ=60)
GTTGTAACAGTGTTGATTTGCCGCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGCTAAGTGAACTGGACATCCCGTAACGTCAGCGAAAAGCGATC > SRR3722132.169532/1‑151 (MQ=60)
AGTGTTGATTTGCCGCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACAC < SRR3722132.35737/151‑1 (MQ=60)
CGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTG < SRR3722132.422719/150‑1 (MQ=60)
CCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCtgtctcttatacacatc > SRR3722132.437909/1‑134 (MQ=60)
GAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCAGAGATACGTACGGC < SRR3722132.301616/151‑1 (MQ=60)
GAACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTCTTGATCCGTTAAGTCAGAGATACGTACGGCAGAGGCAATGACTTGCCCCAGATGCTGAAATGCACCCGTTACT > SRR3722132.504707/1‑151 (MQ=60)
AACTGGACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCAGAGATACGTACGGCAGAGGCAATGACTTGCCCCAGATGCTGAAATGCACCCGTTACTG < SRR3722132.447414/151‑1 (MQ=60)
|
GTTGCGGGTCCCATGCGCGGGTCAGCTGTTGTAACAGTGTTGATTTGCCGCATCCGGTTCGCCCGAGAATCGCTATATGTTCCCCGGCGTTTACCTGAAGAGAAATCCCTTTAAGTGCCTGTTGAGATTGCTCCGGATAAGTGAACTGAACATCCCGTAACGTCAGCGAAACGCGATCGGCAACACGAGTTTGGGTATCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCAGAGATACGTACGGCAGAGGCAATGACTTGCCCCAGATGCTGAAATGCACCCGTTACTG > NZ_CP009273/923472‑923765
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
