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 I208 R1
|
222 |
13.1 |
731276 |
96.6% |
706412 |
85.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,859,998 |
T→C |
I305V (ATT→GTT) |
rpoS ← |
RNA polymerase sigma factor RpoS |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,859,998 | 0 | T | C | 100.0%
| 44.3
/ NA
| 13 | I305V (ATT→GTT) | rpoS | RNA polymerase sigma factor RpoS |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (5/8); total (5/8) |
CGCGGAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAATCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCTTCGTACCCCAGCAAACCGAA > NZ_CP009273/2859923‑2860079
|
cgcgGAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAaca > 1:211468/1‑86 (MQ=255)
cgcgGAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAaca < 2:211468/86‑1 (MQ=255)
ggAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCAc < 1:338653/90‑1 (MQ=255)
tCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCa > 1:154742/1‑90 (MQ=255)
tCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCAc < 1:238826/90‑1 (MQ=255)
tCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCAc < 1:239673/90‑1 (MQ=255)
tCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCAc < 1:78637/90‑1 (MQ=255)
ccTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACg > 1:159785/1‑61 (MQ=255)
ccTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACg < 2:159785/61‑1 (MQ=255)
tGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACa < 2:62576/90‑1 (MQ=255)
tCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGcc < 2:264698/90‑1 (MQ=255)
tCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGGGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGcc > 1:51321/1‑90 (MQ=255)
tCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCTTCGTACCCCAGCAAACCg > 2:284688/1‑90 (MQ=255)
aacctgaacctgGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCTTCGTACCCCAGCAAACCGaa < 2:44326/90‑1 (MQ=255)
|
CGCGGAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAATCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCTTCGTACCCCAGCAAACCGAA > NZ_CP009273/2859923‑2860079
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CTTACTTACTCGCGGAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAATCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCTTCGTACCCCAGCAAACCGAATCGACGTGCCAGCAC > NZ_CP009273/2859913‑2860094
|
CTTACTTACTCGCGGAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTT > SRR3722090.213827/1‑100 (MQ=60)
GGAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCC < SRR3722090.343063/100‑1 (MQ=60)
GAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCA > SRR3722090.156318/1‑100 (MQ=60)
ATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGctgtctcttatacacatct > SRR3722090.161403/1‑81 (MQ=60)
TCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATC < SRR3722090.241666/100‑1 (MQ=60)
TCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATC < SRR3722090.242534/100‑1 (MQ=60)
TCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATC < SRR3722090.79507/100‑1 (MQ=60)
TTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAACCTGGCGAACACGTTCACGGGGGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCC > SRR3722090.51871/1‑100 (MQ=60)
CCTTCAACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCctgtctcttatacacatctccgagcccacgagactcctgag > SRR3722090.62213/1‑59 (MQ=60)
AACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCTTCGTACCCCAGCAAACCGAATCGACGTGCC > SRR3722090.340794/1‑100 (MQ=60)
ACCTGAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCTTCGTACCCCAGCAAACCGAATCGACGTGCCA > SRR3722090.325494/1‑100 (MQ=60)
GAACCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCTTCGTACCCCAGCAAACCGAATCGACGTGCCAGCAC < SRR3722090.34347/100‑1 (MQ=60)
|
CTTACTTACTCGCGGAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCTTCAACCTGAATCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCTTCGTACCCCAGCAAACCGAATCGACGTGCCAGCAC > NZ_CP009273/2859913‑2860094
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
