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 I207 R1
|
218 |
45.0 |
2482936 |
97.1% |
2410930 |
86.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,202,478 |
T→G |
Y345D (TAT→GAT) |
yehP → |
VWA domain‑containing protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,202,478 | 0 | T | G | 100.0%
| 59.6
/ NA
| 19 | Y345D (TAT→GAT) | yehP | VWA domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (12/7); total (12/7) |
TGACGCATCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCTATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCATCATGGCTTGC > NZ_CP009273/2202395‑2202563
|
tGACGCATCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGAcc < 1:1143534/90‑1 (MQ=255)
tGACGCATCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGAcc < 1:487887/90‑1 (MQ=255)
aCGCATCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACcgc > 1:504102/1‑90 (MQ=255)
tCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATAc < 1:1211841/90‑1 (MQ=255)
tCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATAc < 2:642335/90‑1 (MQ=255)
tgtgtCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTg > 1:763389/1‑90 (MQ=255)
gCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAgc > 1:511083/1‑90 (MQ=255)
cgcTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCgg > 2:738975/1‑90 (MQ=255)
gcTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCggg > 2:924745/1‑90 (MQ=255)
tAGCACCGCAACCCCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCt < 1:738975/90‑1 (MQ=255)
gCACCACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAgcc < 2:1236300/63‑1 (MQ=255)
gCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAgcc > 1:1236300/1‑63 (MQ=255)
gCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGcatca > 1:204568/1‑90 (MQ=255)
ttGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCATCATg < 1:476355/84‑1 (MQ=255)
ttGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCATCATg > 2:476355/1‑84 (MQ=255)
ttGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCATCATGGCTTGc > 1:1042746/1‑90 (MQ=255)
ttGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCATCATGGCTTGc > 1:177461/1‑90 (MQ=255)
ttGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCATCATGGCTTGc > 1:922449/1‑90 (MQ=255)
ttGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCATCATGGCTTGc > 2:166607/1‑90 (MQ=255)
|
TGACGCATCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCTATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCATCATGGCTTGC > NZ_CP009273/2202395‑2202563
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 30 ≤ 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
GTTCATCATCATTACTGACGCATCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCTATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCATCATGGCTTGCGGAG > NZ_CP009273/2202380‑2202567
|
GTTCATCATCATTACTGACGCATCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGA < SRR3722089.771567/100‑1 (MQ=60)
ATCATTACTGACGCATCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGC > SRR3722089.510048/1‑100 (MQ=60)
TGACGCATCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGC < SRR3722089.1160934/100‑1 (MQ=60)
TGACGCATCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGC < SRR3722089.493678/100‑1 (MQ=60)
TCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCG < SRR3722089.1230274/100‑1 (MQ=60)
GGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTG > SRR3722089.773622/1‑100 (MQ=60)
GCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGC > SRR3722089.517100/1‑100 (MQ=60)
cgtcggcagcgccagatgtgtataagagacagACCTTGCGATGCCCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGC < SRR3722089.474425/68‑1 (MQ=60)
CGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCtgtctcttatacacat > SRR3722089.1255106/1‑84 (MQ=60)
CGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCATCA > SRR3722089.207155/1‑100 (MQ=60)
TAGCCCCGCAACCCCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCATCATGG < SRR3722089.748647/100‑1 (MQ=60)
CCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCATCATGGCTTGC > SRR3722089.1058362/1‑100 (MQ=60)
CCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCATCATGGCTTGC > SRR3722089.179679/1‑100 (MQ=60)
CCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCATCATGGCTTGC > SRR3722089.935911/1‑100 (MQ=60)
AACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCATCATGGCTTGCGGAG < SRR3722089.482022/100‑1 (MQ=60)
|
GTTCATCATCATTACTGACGCATCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCTATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCATCATGGCTTGCGGAG > NZ_CP009273/2202380‑2202567
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
