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 F3 I95 R1
|
196 |
14.2 |
808436 |
96.0% |
776098 |
85.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,421,635 |
C→G |
A56P (GCA→CCA) |
ytfE ← |
iron‑sulfur cluster repair protein YtfE |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,421,635 | 0 | C | G | 100.0%
| 51.2
/ NA
| 17 | A56P (GCA→CCA) | ytfE | iron‑sulfur cluster repair protein YtfE |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base G (6/11); total (6/11) |
GCGCACGATGATATGGTCGATGATTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGCCAGTTCAGCTTCAATGACCTCAACATCCAGTTCTTTACGTGCCGCCGCGCGCGCCAGCGTCTGCTTACCGCCACAGCAG > NZ_CP009273/4421555‑4421714
|
gcccACGAGGATATGGTCGATGATTTCTGCCAGTGGGGCGCTACGCCAGTCTTTCACAATCGGTTGTTCAGCGAGCTTGGGCAGTTCAGc < 2:358277/87‑1 (MQ=255)
cGATGATATGGTCGATGATTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCaa > 1:256999/1‑90 (MQ=255)
atgatATGGTCGATGATTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATg < 2:365251/90‑1 (MQ=255)
ggTCGATGATTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATGACCTCaa < 1:9226/90‑1 (MQ=255)
cGATGATTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATGACCTCAACAt > 1:402842/1‑90 (MQ=255)
cGATGATTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATGACCTCAACAt > 2:383871/1‑90 (MQ=255)
atgatTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATg > 1:223414/1‑78 (MQ=255)
atgatTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATg < 2:223414/78‑1 (MQ=255)
tCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATGACCTCAACATCCAGTTCt > 2:299669/1‑90 (MQ=255)
ggCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATGACCTCAACATCCAGTTCTTTACGTgccgc > 1:35742/1‑90 (MQ=255)
ggCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATGACCTCAACATCCAGTTCTTTACGTgccgc < 2:216211/90‑1 (MQ=255)
aCGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATGACCTCAACATCCAGTTCTTTACGTGCCGCcgcgcg < 2:143506/90‑1 (MQ=255)
ccAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATGACCTCAACATCCAGTTCTTTACGTGCCGCCgcgcgcgc < 2:402842/90‑1 (MQ=255)
aGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATGACCTCAACATCCAGTTCTTTACGTGCCGCCGCGCGCGCCa < 2:156413/90‑1 (MQ=255)
gttCAGCGAGCTTTGGCAGTTCAGCTTCAATGACCTCAACATCCAGTTCTTTACGTGCCGCCGCGCGCGCCAGCGTCTGCTTACCGCcac < 1:137034/90‑1 (MQ=255)
gCGAGCTTTGGCAGTTCAGCTTCAATGCCCTCAACATCCAGTTCTTTACGTGCCGCCGCGCGCGCCAGCGTCTGCTTACCGCCAcagcag < 2:9265/90‑1 (MQ=255)
gCGAGCTTTGGCAGTTCAGCTTCAATGACCTCAACATCCAGTTCTTTACGTGCCGCCGCGCGCGCCAGCGTCTGCTTACCGCCAcagcag < 1:295428/90‑1 (MQ=255)
|
GCGCACGATGATATGGTCGATGATTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGCCAGTTCAGCTTCAATGACCTCAACATCCAGTTCTTTACGTGCCGCCGCGCGCGCCAGCGTCTGCTTACCGCCACAGCAG > NZ_CP009273/4421555‑4421714
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GCGGTGACGATCGTGGTAGCGCACGATGATATGGTCGATGATTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGCCAGTTCAGCTTCAATGACCTCAACATCCAGTTCTTTACGTGCCGCCGCGCGCGCCAGCGTCTGCTTACCGCCACAGCAGTAATCCATATCAT > NZ_CP009273/4421537‑4421727
|
GCGGTGACGATCGTGGTAGCGCACGATGATATGGTCGATGATTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGC < SRR3722235.152442/100‑1 (MQ=60)
GCGGTGACGATCGTGGTAGCGCACGATGATATGGTCGATGATTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGC < SRR3722235.231084/100‑1 (MQ=60)
TGGTAGCGCACGATGATATGGTCGATGATTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAA > SRR3722235.260369/1‑100 (MQ=60)
ATGATATGGTCGATGATTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATGACCTCAACAT > SRR3722235.408649/1‑100 (MQ=60)
GATATGGTCGATGATTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATGACCTCAACATCT > SRR3722235.226222/1‑100 (MQ=60)
GGTCGATGATTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATGACCTCAACATCCAGTTC < SRR3722235.9326/100‑1 (MQ=60)
CTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATGACCTCAACATCCAGTTCTTTACGTGCCGC > SRR3722235.36133/1‑100 (MQ=60)
GTTCAGCGAGCTTTGGCAGTTCAGCTTCAATGACCTCAACATCCAGTTCTTTACGTGCCGCCGCGCGCGCCAGCGTCTGCTTACCGCCACAGCAGTAATC < SRR3722235.138634/100‑1 (MQ=60)
GCGAGCTTTGGCAGTTCAGCTTCAATGACCTCAACATCCAGTTCTTTACGTGCCGCCGCGCGCGCCAGCGTCTGCTTACCGCCACAGCAGTAATCCATAT < SRR3722235.299543/100‑1 (MQ=60)
AGCTTTGGCAGTTCAGCTTCAATGACCTCAACATCCAGTTCTTTACGTGCCGCCGCGCGCGCCAGCGTCTGCTTACCGCCACAGCAGTAATCCATATCAT > SRR3722235.23617/1‑100 (MQ=60)
|
GCGGTGACGATCGTGGTAGCGCACGATGATATGGTCGATGATTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGCCAGTTCAGCTTCAATGACCTCAACATCCAGTTCTTTACGTGCCGCCGCGCGCGCCAGCGTCTGCTTACCGCCACAGCAGTAATCCATATCAT > NZ_CP009273/4421537‑4421727
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
