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 |
4,352,635 |
C→G |
S164T (AGC→ACC) |
yjdC ← |
transcriptional regulator |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,352,635 | 0 | C | G | 100.0%
| 82.7
/ NA
| 24 | S164T (AGC→ACC) | yjdC | transcriptional regulator |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base G (15/9); total (15/9) |
GTCAGGTCAATGCACCACCCTGGCGGCAGCGGGCGAAGCGCAGGATATCTTCCGCCAGCCGATGTGCAGTGTCGACATCCGCCTGGCTACGATTCACCAGCATTCGGCTTAAACAGCCTTCCAGCACCAGTTCCATCTGCTTTGCTACCATCGCCGGATCGTCAACTTCCAG > NZ_CP009273/4352549‑4352720
|
gTCAGGTCAATGCACCACCCTGGCGGCAGCGGGCGAAGCGCAGGATATCTTCCGCCAGCCGATGTGCAGTGTCGACATCCGCCTGGGTAc < 1:512806/90‑1 (MQ=255)
gTCAGGTCAATGCACCACCCTGGCGGCAGCGGGCGAAGCGCAGGATATCTTCCGCCAGCCGATGTGCAGTGTCGACATCCGCCTGGGTAc < 1:76201/90‑1 (MQ=255)
cAGGTCAATGCACCACCCTGGCGGCAGCGGGCGAAGCGCAGGATATCTTCCGCCAGCCGATGTGCAGTGTCGACATCCGCCTGGGTACGa > 1:474087/1‑90 (MQ=255)
cAGGTCAATGCACCACCCTGGCGGCAGCGGGCGAAGCGCAGGATATCTTCCGCCAGCCGATGTGCAGTGTCGACATCCGCCTGGGTACGa > 2:720402/1‑90 (MQ=255)
cAATGCACCACCCTGGCGGCAGCGGGCGAAGCGCAGGATATCTTCCGCCAGCCGATGTGCAGTGTCGACATCCGCCTGGGTACGATTCAc > 2:385325/1‑90 (MQ=255)
ccaccCTGGCGGCAGCGGGCGACGCGAAGGATATCTTCCGCCAGCCGATGTGCAGTGTCGACATCCGCCTGGGTACGATTCACCAGCAtt < 1:196871/90‑1 (MQ=255)
caccCTGGCGGCAGCGGGCGAAGCGCAGGATATCTTCCGCCAGCCGATGTGCAGTGTCGACATCCGCCTGGGTACGATTCACCAGCATTc > 1:77684/1‑90 (MQ=255)
cTGGCGGCAGCGGGCGAAGCGCAGGATATCTTCCGCCAGCCGATGTGCAGTGTCGACATCCGCCTGGGTACGATTCACCAGCATTCGGCt > 1:422812/1‑90 (MQ=255)
cTGGCGGCAGCGGGCGAAGCGCAGGATATCTTCCGCCAGCCGATGTGCAGTGTCGACATCCGCCTGGGTACGATTCACCAGCATTCGGCt > 1:607074/1‑90 (MQ=255)
cTGGCGGCAGCGGGCGAAGCGCAGGATATCTTCCGCCAGCCGATGTGCAGTGTCGACATCCGCCTGGGTACGATTCACCAGCATTCGGCt > 1:72255/1‑90 (MQ=255)
cTGGCGGCAGCGGGCGAAGCGCAGGATATCTTCCGCCAGCCGATGTGCAGTGTCGACATCCGCCTGGGTACGATTCACCAGCATTCGGCt > 1:730124/1‑90 (MQ=255)
gcggcAGCGGGCGAAGCGCAGGATATCTTCCGCCAGCCGATGTGCAGTGTCGACATCCGCCTGGGTACGATTCACCAGCATTCGGCTTaa < 2:506364/90‑1 (MQ=255)
cGAAGCGCAGGATATCTTCCGCCAGCCGATGTGCAGTGTCGACATCCGCCTGGGTACGATTCACCAGCATTCGGCTTAAACAGCCTTCCa < 2:441996/90‑1 (MQ=255)
gCCAGCCGATGTGCAGTGTCGACATCCGCCTGGGTACGATTCACCAGCATTCGGCTTAAACAGcc < 2:174486/65‑1 (MQ=255)
gCCAGCCGATGTGCAGTGTCGACATCCGCCTGGGTACGATTCACCAGCATTCGGCTTAAACAGcc > 1:174486/1‑65 (MQ=255)
gtgtCGACATCCGCCTGGGTACGATTCACCAGCATTCGGCTTAAACAGCCTTCCAGCACCAGTTCCATCTGCTTTGCTACCATCGCCGGa > 1:322229/1‑90 (MQ=255)
gtgtCGACATCCGCCTGGGTACGATTCACCAGCATTCGGCTTAAACAGCCTTCCAGCACCAGTTCCATCTGCTTTGCTACCATCGCCGGa > 2:287693/1‑90 (MQ=255)
gtCGACATCCGCCTGGGTACGATTCACCAGCATTCGGCTTAAACAGCCTTCCAGCACCAGTTCCATCTGCTTTGCTACCATCGCCGGATc > 1:114216/1‑90 (MQ=255)
cGACATCCGCCTGGGTACGATTCACCAGCATTCGGCTTAAACAGCCTTCCAGCACCAGTTCCATCTGCTTTGCTACCATCGCCGGATCGt < 2:353487/90‑1 (MQ=255)
ccGCCTGGGTACGATTCACCAGCATTCGGCTTAAACAGCCTTCCAGCACCAGTTCCATCTGCTTTGCTACCATCGCCGGATCGTCAACtt > 2:90923/1‑90 (MQ=255)
gCCTGGGTACGATTCACCAGCATTCGGCTTAAACAGCCTTCCAGCACCAGTTCCATCTGCTTTGCTACCATCGCCGGATCGTCAACTTcc > 2:335312/1‑90 (MQ=255)
gCCTGGGTACGATTCACCAGCATTCGGCTTAAACAGCCTTCCAGCACCAGTTCCATCTGCTTTGCTACCATCGCCGGATCGTCAACTTcc > 1:708409/1‑90 (MQ=255)
cTGGGTACGATTCACCAGCATTCGGCTTAAACAGCCTTCCAGCACCAGTTCCATCTGCTTTGCTACCATCGCCGGATCGTCAACTTCCAg < 2:65142/90‑1 (MQ=255)
cTGGGTACGATTCACCAGCATTCGGCTTAAACAGCCTTCCAGCACCAGTTCCATCTGCTTTGCTACCATCGCCGGATCGTCAACTTCCAg < 1:158893/90‑1 (MQ=255)
|
GTCAGGTCAATGCACCACCCTGGCGGCAGCGGGCGAAGCGCAGGATATCTTCCGCCAGCCGATGTGCAGTGTCGACATCCGCCTGGCTACGATTCACCAGCATTCGGCTTAAACAGCCTTCCAGCACCAGTTCCATCTGCTTTGCTACCATCGCCGGATCGTCAACTTCCAG > NZ_CP009273/4352549‑4352720
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ 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
TTCTGTGTTTCTGTCAGGTCAATGCACCACCCTGGCGGCAGCGGGCGAAGCGCAGGATATCTTCCGCCAGCCGATGTGCAGTGTCGACATCCGCCTGGCTACGATTCACCAGCATTCGGCTTAAACAGCCTTCCAGCACCAGTTCCATCTGCTTTGCTACCATCGCCGGATCGTCAACTTCCAGTGTGGTTAACAG > NZ_CP009273/4352537‑4352732
|
TTCTGTGTTTCTGTCAGGTCAATGCACCCCCCTGGCGGCAGCGGGCGAAGCGCGGGATATCTTCCGCCAGCCGATGTGCAGTGTCGACATCCGCCTGGGT < SRR3722073.336581/100‑1 (MQ=60)
gtgtataagagacagGGTCAATGCCCCCCCCTGGCGGCAGCGGGCGAAGCGCAGGATATCTTCCGCCAGCCGATGTGCAGTGTCGACATCCGCCTGGGTA < SRR3722073.89691/85‑1 (MQ=60)
GTGTTTCTGTCAGGTCAATGCACCACCCTGGCGGCAGCGGGCGAAGCGCAGGATATCTTCCGCCAGCCGATGTGCAGTGTCGACATCCGCCTGGGTACGA > SRR3722073.484183/1‑100 (MQ=60)
GTCAGGTCAATGCACCACCCTGGCGGCAGCGGGCGAAGCGCAGGATATCTTCCGCCAGCCGATGTGCAGTGTCGACATCCGCCTGGGTACGATTCACCAG < SRR3722073.523613/100‑1 (MQ=60)
GTCAGGTCAATGCACCACCCTGGCGGCAGCGGGCGAAGCGCAGGATATCTTCCGCCAGCCGATGTGCAGTGTCGACATCCGCCTGGGTACGATTCACCAG < SRR3722073.77957/100‑1 (MQ=60)
GTCAATGCACCACCCTGGCGGCAGCGGGCGAAGCGCAGGATATCTTCCGCCAGCCGATGTGCAGTGTCGACATCCGCCTGGGTACGATTCACCAGCATTC > SRR3722073.79464/1‑100 (MQ=60)
ATGCACCACCCTGGCGGCAGCGGGCGAAGCGCAGGATATCTTCCGCCAGCCGATGTGCAGTGTCGACATCCGCCTGGGTACGATTCACCAGCATTCGGCT > SRR3722073.431864/1‑100 (MQ=60)
ATGCACCACCCTGGCGGCAGCGGGCGAAGCGCAGGATATCTTCCGCCAGCCGATGTGCAGTGTCGACATCCGCCTGGGTACGATTCACCAGCATTCGGCT > SRR3722073.619718/1‑100 (MQ=60)
ATGCACCACCCTGGCGGCAGCGGGCGAAGCGCAGGATATCTTCCGCCAGCCGATGTGCAGTGTCGACATCCGCCTGGGTACGATTCACCAGCATTCGGCT > SRR3722073.73930/1‑100 (MQ=60)
ATGCACCACCCTGGCGGCAGCGGGCGAAGCGCAGGATATCTTCCGCCAGCCGATGTGCAGTGTCGACATCCGCCTGGGTACGATTCACCAGCATTCGGCT > SRR3722073.744861/1‑100 (MQ=60)
CCACCCTGGCGGCAGCGGGCGACGCGAAGGATATCTTCCGCCAGCCGATGTGCAGTGTCGACATCCGCCTGGGTACGATTCACCAGCATTCGGCTTAAAC < SRR3722073.200815/100‑1 (MQ=60)
GATATCTTCCGCCAGCCGATGTGCAGTGTCGACATCCGCCTGGGTACGATTCACCAGCATTCGGCTTAAACAGCCTTCCAGCACCctgtctcttatacac > SRR3722073.177890/1‑85 (MQ=60)
CCGATGTGCAGTGTCGACATCCGCCTGGGTACGATTCACCAGCATTCGGCTTAAACAGCCTTCCAGCACCAGTTCCATCTGCTTTGCTACCATCGCCGGA > SRR3722073.329065/1‑100 (MQ=60)
GATGTGCAGTGTCGACATCCGCCTGGGTACGATTCACCAGCATTCGGCTTAAACAGCCTTCCAGCACCAGTTCCATCTGCTTTGCTACCATCGCCGGATC > SRR3722073.116673/1‑100 (MQ=60)
GTCGACATCCGCCTGGGTACGATTCACCAGCATTCGGCTTAAACAGCCTTCCAGCACCAGTTCCATCTGCTTTGCTACCATCGCCGGATCGTCAACTTCC > SRR3722073.722731/1‑100 (MQ=60)
ACATCCGCCTGGGTACGATTCACCAGCATTCGGCTTAAACAGCCTTCCAGCACCAGTTCCATCTGCTTTGCTACCATCGCCGGATCGTCAACTTCCAGTG > SRR3722073.628985/1‑100 (MQ=60)
CTGGGTACGATTCACCAGCATTCGGCTTAAACAGCCTTCCAGCACCAGTTCCATCTGCTTTGCTACCATCGCCGGATCGTCAACTTCCAGTGTGGTTAAC < SRR3722073.162105/100‑1 (MQ=60)
GGGTACGATTCACCAGCATTCGGCTTAAACAGCCTTCCAGCACCAGTTCCATCTGCTTTGCTACCATCGCCGGATCGTCAACTTCCAGTGTGGTTAACAG < SRR3722073.302634/100‑1 (MQ=60)
GGGTACGATTCACCAGCATTCGGCTTAAACAGCCTTCCAGCACCAGTTCCATCTGCTTTGCTACCATCGCCGGATCGTCAACTTCCAGTGTGGTTAACAG < SRR3722073.734957/100‑1 (MQ=60)
|
TTCTGTGTTTCTGTCAGGTCAATGCACCACCCTGGCGGCAGCGGGCGAAGCGCAGGATATCTTCCGCCAGCCGATGTGCAGTGTCGACATCCGCCTGGCTACGATTCACCAGCATTCGGCTTAAACAGCCTTCCAGCACCAGTTCCATCTGCTTTGCTACCATCGCCGGATCGTCAACTTCCAGTGTGGTTAACAG > NZ_CP009273/4352537‑4352732
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
