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 |
3,771,044 |
A→G |
K96E (AAA→GAA) |
lldP → |
L‑lactate permease |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,771,044 | 0 | A | G | 100.0%
| 102.3
/ NA
| 29 | K96E (AAA→GAA) | lldP | L‑lactate permease |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (15/14); total (15/14) |
TTCTTCTACGGGTTGTGGCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGAAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCTGCAAATGCTGATCGTCGGTTTCTG > NZ_CP009273/3770975‑3771129
|
ttcttcTACGGGTTGTGGCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGAcatc > 2:345768/1‑90 (MQ=255)
ttcttcTACGGGTTGTGGCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGAcatc > 2:168118/1‑90 (MQ=255)
tctACGGGTTGTGGCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTc < 2:32684/90‑1 (MQ=255)
tACGGGTTGTGGCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGc < 1:15363/90‑1 (MQ=255)
aCGGGTTGTGGCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCt > 2:524568/1‑90 (MQ=255)
tgtgGCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTa < 2:128792/90‑1 (MQ=255)
gtgGCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTAt > 2:593662/1‑90 (MQ=255)
cccATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCtt < 2:163994/90‑1 (MQ=255)
ccATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCttt < 1:524568/90‑1 (MQ=255)
cATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGc < 1:277982/59‑1 (MQ=255)
cATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGc > 2:277982/1‑59 (MQ=255)
gngTGGNNNANTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATa < 1:222252/90‑1 (MQ=255)
gcgTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATa < 2:97047/90‑1 (MQ=255)
gcgTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATa < 2:436677/90‑1 (MQ=255)
gcgTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATa < 1:579036/90‑1 (MQ=255)
gcgTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATa < 1:208887/90‑1 (MQ=255)
attattGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGAc > 2:408053/1‑90 (MQ=255)
attGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAg > 1:507411/1‑90 (MQ=255)
ttGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGc > 2:426709/1‑90 (MQ=255)
aGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCt > 1:725205/1‑90 (MQ=255)
gCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCTg > 2:557008/1‑90 (MQ=255)
cGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCTGc < 1:532580/90‑1 (MQ=255)
ggTGTTCGTCTATAAGATCTCGGTGGTACCCGTATCGTTTAAAAACATTCGCTCGTCGATTCTTTCGAGAACCCCTGCCCAGCGTCTGCa > 1:218960/1‑90 (MQ=255)
gtTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCTGCAAAt < 2:507411/90‑1 (MQ=255)
gtTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGAAATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCTGCAAAt > 1:76690/1‑90 (MQ=255)
cTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCTGCAAATGCTGAt < 2:86694/90‑1 (MQ=255)
ataAGAACTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCTGCAAATGCTGAtcg > 2:413136/1‑90 (MQ=255)
cGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCTGCAAATGCTGATCGTCGGTTTCt > 2:144939/1‑90 (MQ=255)
ggTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCTGCAAATGCTGATCGTCGGTTTCTg > 2:279647/1‑90 (MQ=255)
|
TTCTTCTACGGGTTGTGGCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGAAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCTGCAAATGCTGATCGTCGGTTTCTG > NZ_CP009273/3770975‑3771129
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ 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
CTAACGCGCTGGCCTCGGTGGTTTATGGTTTCTTCTACGGGTTGTGGCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGAAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCTGCAAATGCTGATCGTCGGTTTCTGTTTCGGCGCGT > NZ_CP009273/3770946‑3771140
|
CTAACGCGCTGGCCTCGGTGGTTTATGGTTTCTTCTACGGGTTGTGGCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGA > SRR3722073.167262/1‑100 (MQ=60)
tcagatgtgtataagagacaGGGTTGTGGCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACAT < SRR3722073.283862/80‑1 (MQ=60)
ccgagatctacacactgcatatcgtcggcagcgtcagatgtgtataagagacagGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCT < SRR3722073.301000/46‑1 (MQ=60)
TACGGGTTGTGGCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTC < SRR3722073.15754/100‑1 (MQ=60)
CCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCC < SRR3722073.535577/100‑1 (MQ=60)
GNGTGGNNNANTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACC < SRR3722073.226858/100‑1 (MQ=60)
GCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACC < SRR3722073.213170/100‑1 (MQ=60)
GCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACC < SRR3722073.591131/100‑1 (MQ=60)
GTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAG > SRR3722073.518117/1‑100 (MQ=60)
TCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCT > SRR3722073.739842/1‑100 (MQ=60)
TTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGTACCCGTATCGTTTAAAAACATTCGCTCGTCGATTCTTTCGAGAACCCCTGCCCAGCGTCTGCA > SRR3722073.223479/1‑100 (MQ=23)
TTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGAAATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCTGCAAAT > SRR3722073.78454/1‑100 (MQ=60)
CGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCTGCAAATGCTGAT < SRR3722073.543701/100‑1 (MQ=60)
GTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCTGCAAATGCTGATCGTCGGTTTCTGTTTCGGCGCGT > SRR3722073.288086/1‑100 (MQ=60)
|
CTAACGCGCTGGCCTCGGTGGTTTATGGTTTCTTCTACGGGTTGTGGCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGAAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCTGCAAATGCTGATCGTCGGTTTCTGTTTCGGCGCGT > NZ_CP009273/3770946‑3771140
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
