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 I209 R1
|
216 |
14.4 |
815930 |
96.1% |
784108 |
85.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,818,451 |
T→C |
E162G (GAA→GGA) |
mltB ← |
lytic murein transglycosylase B |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,818,451 | 0 | T | C | 100.0%
| 38.6
/ NA
| 13 | E162G (GAA→GGA) | mltB | lytic murein transglycosylase B |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (2/11); total (2/11) |
TACTCCGCGCGGCGTGGGTAGTTAAATGACAGCGTTGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTTCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACCTGCCACGCGCGATTCAACGCATCTTCATACTGATTCC > NZ_CP009273/2818364‑2818535
|
tACTCCGCGCGGCGTGGGTAGTTAAATGACAGCGTTGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTCCa < 1:110454/90‑1 (MQ=255)
tCCGCGCGGCGTGGGTAGTTAAATGACAGCGTTGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTCCAACg < 1:237488/90‑1 (MQ=255)
tCCGCGCGGCGTGGGTAGTTAAATGACAGCGTTGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTCCAACg < 2:328304/90‑1 (MQ=255)
ccGCGCGGCGTGGGTAGTTAAATGACAGCGTTGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTCCAACGc > 1:123230/1‑90 (MQ=255)
gggTAGTTAAATGACAGCGTTGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCcg < 1:86100/90‑1 (MQ=255)
gCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACCTGCCAcgc < 1:42801/90‑1 (MQ=255)
ttttCCCCATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACCTGCCACGCGCGAt < 1:15575/90‑1 (MQ=255)
ttCCCCATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACCTGCCACGCGCGATTc < 2:38520/90‑1 (MQ=255)
cATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCCGGCGGTTCTCCATACACCTGCCACGCGCGATTCAACGc < 2:123230/90‑1 (MQ=255)
cATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACCTGCCACGCGCGATTCAACGc < 1:98999/90‑1 (MQ=255)
aTCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACCTGCCACGCGCGATTCAACGCa > 2:73603/1‑90 (MQ=255)
tCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACCTGCCACGCGCGATTCAACGCAt < 1:41415/90‑1 (MQ=255)
gggTTCCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACCTGCCACGCGCGATTCAACGCATCTTCATACTGATTcc < 2:106644/90‑1 (MQ=255)
|
TACTCCGCGCGGCGTGGGTAGTTAAATGACAGCGTTGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTTCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACCTGCCACGCGCGATTCAACGCATCTTCATACTGATTCC > NZ_CP009273/2818364‑2818535
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ 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
GAGAAATACTCCGCGCGGCGTGGGTAGTTAAATGACAGCGTTGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTTCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACCTGCCACGCGCGATTCAACGCATCTTCATACTGATTCCAGAAAACCACACC > NZ_CP009273/2818358‑2818548
|
GAGAAATACTCCGCGCGGCGTGGGTAGTTAAATGATAGCGTTGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTCCAACGC < SRR3722091.38956/100‑1 (MQ=60)
GAGAAATACTCCGCGCGGCGTGGGTAGTTAAATGACAGCGTTGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTCCAACGC > SRR3722091.125089/1‑100 (MQ=60)
TACTCCGCGCGGCGTGGGTAGTTAAATGACAGCGTTGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTCCAACGCCGATAA < SRR3722091.112142/100‑1 (MQ=60)
TCCGCGCGGCGTGGGTAGTTAAATGACAGCGTTGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCC < SRR3722091.241144/100‑1 (MQ=60)
GGGTAGTTAAATGACAGCGTTGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTT < SRR3722091.87430/100‑1 (MQ=60)
GCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACCTGCCACGCGCGATTCAAC < SRR3722091.43417/100‑1 (MQ=60)
TTTTCCCCATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACCTGCCACGCGCGATTCAACGCATC < SRR3722091.15798/100‑1 (MQ=60)
CATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACCTGCCACGCGCGATTCAACGCATCTTCATAC < SRR3722091.100528/100‑1 (MQ=60)
TCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACCTGCCACGCGCGATTCAACGCATCTTCATACTG < SRR3722091.42008/100‑1 (MQ=60)
TTCCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACCTGCCACGCGCGATTCAACGCATCTTCATACTGATTCCAGAAAACCACACC > SRR3722091.58875/1‑100 (MQ=60)
|
GAGAAATACTCCGCGCGGCGTGGGTAGTTAAATGACAGCGTTGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTTCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACCTGCCACGCGCGATTCAACGCATCTTCATACTGATTCCAGAAAACCACACC > NZ_CP009273/2818358‑2818548
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
