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 |
|
A2 F5 I184 R1
|
278 |
29.6 |
1166432 |
97.3% |
1134938 |
124.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
977,344 |
A→G |
D281G (GAC→GGC) |
ldtD → |
L,D‑transpeptidase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 977,344 | 0 | A | G | 100.0%
| 66.6
/ NA
| 19 | D281G (GAC→GGC) | ldtD | L,D‑transpeptidase |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (8/11); total (8/11) |
CGCCCAGGGCAGTGGAGTAACGACGTACCGGCGTTGCGCGAAATATTGCAACGCACAGGCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGACGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGATGGATAAGCAAACGACGTCTCGTAGTAAACCTGCGCCTGCCGTTCGCGCCGCCTACGATA > NZ_CP009273/977232‑977457
|
cgcCCAGGGCAGTGGAGTAACGACGTACCGGCGTTGCGCGAAATATTGCAACGCACAGGCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGtt < 2:413671/138‑1 (MQ=255)
gAGTAACGACGTACCGGCGTTGCGCGAAATATTGCAACGCACAGGCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAAcagca < 1:328618/139‑1 (MQ=255)
acgTACCGGCGTTGCGCGAAATATTGCAACGCACAGGCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACt > 1:249606/1‑137 (MQ=255)
tACCGGCGTTGCGCGAAATATTGCAACGCACAGGCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGcc > 1:81284/1‑139 (MQ=255)
tACCGGCGTTGCGCGAAATATTGCAACGCACAGGCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCAATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGcc > 2:579357/1‑139 (MQ=255)
ttGCAACGCACAGGCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGGTGGATAAGCAAACGACGt < 1:232553/139‑1 (MQ=255)
cAACGCACAGGCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGATGGATAAGCAAACGACGtct < 2:249606/138‑1 (MQ=255)
cGCACAGGCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGATGGATAAGCAAACGACGTCTCg > 2:545354/1‑137 (MQ=255)
cGCACAGGCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGATGGATAAGCAAACGACGTCTCg > 2:175493/1‑137 (MQ=255)
cGCACAGGCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGATGGATAAGCAAACGACGTCTCg > 2:245430/1‑137 (MQ=255)
gCACAGGCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGATGGATAAGCAAACGACGTCTCgtag < 1:245430/139‑1 (MQ=255)
gggCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGATGGATAAGCAAACGACGTCTCGTAGTAAACCTGCGCCTGCCGTTc > 1:579069/1‑139 (MQ=255)
ggCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCg < 2:454429/92‑1 (MQ=255)
ggCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCg > 1:454429/1‑92 (MQ=255)
ccGAAAATTCCTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGATGGATAAGCAAACGACGTCTCGTAGTAAACCTGCGCCTGCCGTTcgcg < 2:241210/139‑1 (MQ=255)
ccGAAAATTACTCTCCCTGGCGATGACACGCCAACTGGCGCGGTAGGCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGATGGATAAGCAAACGACGTCTCGTAGTAAACCTGCGCCTGCCGTTcgcg < 2:389522/139‑1 (MQ=255)
ccGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGATGGATAAGCAAACGACGTCTCGTAGTAAACCTGCGCCTGCCGTTcgcg < 1:545354/139‑1 (MQ=255)
ccGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGATGGATAAGCAAACGACGTCTCGTAGTAAACCTGCGCCTGCCGTTcgcg < 1:501537/139‑1 (MQ=255)
ccTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGAGGGATAAGCAAACGACGTCTCGTAGTAAACCGGCGCCTGCCGTTCGCGCCGCCTACGATa < 2:81284/136‑1 (MQ=255)
|
CGCCCAGGGCAGTGGAGTAACGACGTACCGGCGTTGCGCGAAATATTGCAACGCACAGGCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGACGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGATGGATAAGCAAACGACGTCTCGTAGTAAACCTGCGCCTGCCGTTCGCGCCGCCTACGATA > NZ_CP009273/977232‑977457
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GTGGAGTAACGACGTACCGGCGTTGCGCGAAATATTGCAACGCACAGGCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGACGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGATGGATAAGCAAACGACGTCTCGTAGTAAACCTGCGCCTGCCGTTCGCGCCGCCTACGAT > NZ_CP009273/977243‑977456
|
GTGGAGTAACGACGTACCGGCGTTGCGCGAAATATTGCAACGCACAGGCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTA > SRR3722139.252767/1‑149 (MQ=60)
GGAGTAACGACGTACCGGCGTTGCGCGAAATATTGCAACGCACAGGCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCC < SRR3722139.332645/151‑1 (MQ=60)
GAGTAACGACGTACCGGCGTTGCGCGAAATATTGCAACGCACAGGCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCG > SRR3722139.82227/1‑151 (MQ=60)
ATTGCAACGCACAGGCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGGTGGATAAGCAAACGACGTCTCGTAGTAAA < SRR3722139.235422/151‑1 (MQ=60)
CGCACAGGCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGATGGATAAGCAAACGACGTCTCGTAGTAAACCTGCGC < SRR3722139.248490/151‑1 (MQ=60)
TGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGATGGATAAGCAAACGACGTCTCGTAGTAAACCTGCGCCTGCCGTTCG > SRR3722139.585667/1‑151 (MQ=60)
GTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGATGGATAAGCActgtctcttatacacatctccgagcccacgagaccgt > SRR3722139.459750/1‑114 (MQ=60)
GCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGATGGATAAGCAAACGACGTCTCGTAGTAAACCTGCGCCTGCCGTTCGCGCCGCCTACGAT < SRR3722139.507327/151‑1 (MQ=60)
GCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGATGGATAAGCAAACGACGTCTCGTAGTAAACCTGCGCCTGCCGTTCGCGCCGCCTACGAT < SRR3722139.551626/151‑1 (MQ=60)
|
GTGGAGTAACGACGTACCGGCGTTGCGCGAAATATTGCAACGCACAGGCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGACGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGATGGATAAGCAAACGACGTCTCGTAGTAAACCTGCGCCTGCCGTTCGCGCCGCCTACGAT > NZ_CP009273/977243‑977456
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
