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 I195 R1
|
222 |
27.1 |
1551108 |
96.0% |
1489063 |
86.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,661,508 |
T→G |
T250P (ACC→CCC) |
hcaR ← |
DNA‑binding transcriptional regulator HcaR |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,661,508 | 0 | T | G | 100.0%
| 56.9
/ NA
| 17 | T250P (ACC→CCC) | hcaR | DNA‑binding transcriptional regulator HcaR |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (10/7); total (10/7) |
CGGCTTCATCTCCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGTATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTCACCAGAATATTCGTTG > NZ_CP009273/2661422‑2661591
|
cGGCTTCATCTCCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGAtt > 2:749175/1‑90 (MQ=255)
gCTTCATCTCCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTaa > 1:225633/1‑90 (MQ=255)
cATCTCCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAatt > 1:722078/1‑90 (MQ=255)
aTCTCCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAatta < 2:9402/90‑1 (MQ=255)
tctcCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAattat < 1:628979/90‑1 (MQ=255)
tcttcCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAAc < 1:257889/90‑1 (MQ=255)
ccACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCggg < 2:47461/90‑1 (MQ=255)
cACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGt > 1:605503/1‑90 (MQ=255)
aaTGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAg > 1:425857/1‑90 (MQ=255)
aTGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAattat > 1:339200/1‑58 (MQ=255)
aTGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAattat < 2:339200/58‑1 (MQ=255)
aGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCAt > 2:204986/1‑90 (MQ=255)
ggCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATg > 1:215025/1‑90 (MQ=255)
tttCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCccacc > 2:118711/1‑90 (MQ=255)
ggACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTc < 2:234381/90‑1 (MQ=255)
aacaacCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTCACCAGAat < 2:734052/90‑1 (MQ=255)
gTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGCGACGCCCAGCCCCATGCCCACCAGATTCATGGTCACCAGAATATTCGTTg > 1:388244/1‑90 (MQ=255)
|
CGGCTTCATCTCCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGTATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTCACCAGAATATTCGTTG > NZ_CP009273/2661422‑2661591
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ 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
CGTAATGCCGGCTTCATCTCCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGTATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTCACCAGAATATTCGTTGCCACCTGGACGATATT > NZ_CP009273/2661414‑2661607
|
CGTAATGCCGGCTTCATCTCCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAA > SRR3722073.230340/1‑100 (MQ=60)
AATGCCGGCTTCATCTCCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAAT < SRR3722073.720657/100‑1 (MQ=60)
ATGCCGGCTTCATCTCCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATT < SRR3722073.51965/100‑1 (MQ=60)
ATGCCGGCTTCATCTCCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATT > SRR3722073.736670/1‑100 (MQ=60)
TCTCCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACC < SRR3722073.642013/100‑1 (MQ=60)
CCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGT > SRR3722073.618111/1‑100 (MQ=60)
TCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAA < SRR3722073.263313/100‑1 (MQ=60)
TCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAG > SRR3722073.434969/1‑100 (MQ=60)
CAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCctgtctcttatacacatctgac > SRR3722073.346400/1‑78 (MQ=60)
AGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATG > SRR3722073.219460/1‑100 (MQ=60)
AAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGCGACGCCCAGCCCCATGCCCACCAGATTCATGGTCACCAGAATATTCGTTG > SRR3722073.396510/1‑100 (MQ=60)
AAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGctgtctcttatacacatctgacgctgccgacgatatgcagtgtgtagatctc > SRR3722073.268590/1‑48 (MQ=60)
GGATTAAAATTATTCATATAACCGGGTATCAAAGAGACGCCCAGCCCCATGCCCACCAGATTCATGGTCACCAGAATATTCGTTGCCACCTGGACGATAT > SRR3722073.711064/1‑100 (MQ=60)
GATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTCACCAGAATATTCGTTGCCACCTGGACGATATT > SRR3722073.594173/1‑100 (MQ=60)
|
CGTAATGCCGGCTTCATCTCCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGTATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTCACCAGAATATTCGTTGCCACCTGGACGATATT > NZ_CP009273/2661414‑2661607
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
