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 I225 R1
|
227 |
21.4 |
1179702 |
97.1% |
1145490 |
86.5 |
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 | 96.0%
| 69.6
/ ‑3.4
| 25 | E162G (GAA→GGA) | mltB | lytic murein transglycosylase B |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base C (3/21); total (3/22) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.87e-01 |
GCGCGGCGTGGGTAGTTAAATGACAGCGTTGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTTCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACCTGCCACGCGCGATTCAACGC > NZ_CP009273/2818370‑2818518
|
gcgcgGCGTGGGTAGTTAAATGACAGCGTTGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTCCAACGCCg > 2:483087/1‑90 (MQ=255)
gcgTGGGTAGTTAAATGACAGCGTTGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTCCAACGCCGATAAt > 2:197515/1‑90 (MQ=255)
gggTAGTTAAATGACAGCGTTGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCcg < 2:214612/90‑1 (MQ=255)
gACAGCGTTGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTcc < 1:37244/90‑1 (MQ=255)
aGCGTTGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCcggc < 1:64676/90‑1 (MQ=255)
ttGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCCGGCGGTa < 1:317165/90‑1 (MQ=255)
ttGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCCGGCGGTa < 1:450351/90‑1 (MQ=255)
ttGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCCGGCGGTa < 2:544063/90‑1 (MQ=255)
taccAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCCGGCGGTAc < 1:460634/88‑1 (MQ=255)
tGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCCGGCGGTAc < 2:431117/90‑1 (MQ=255)
tGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCCGGCGGTAc < 2:132951/90‑1 (MQ=255)
tGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCCGGCGGTAc < 1:107451/90‑1 (MQ=255)
aGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCcgac > 2:264456/1‑68 (MQ=255)
aGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCcgac < 1:264456/68‑1 (MQ=255)
gcgcATCGAGGATGCGAGTTTTCCCCATCCCGCCCCCCCAGCGGGTTCCACCGCCGATAACCCCGACGATAATTTCCGGCGGTACTCCAt < 1:423305/90‑1 (MQ=255)
aGTTTTCCCCATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACCTGCCAcgcgcg < 2:375529/90‑1 (MQ=255)
tCCCCATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACCTGCCACGCGCGATTCa < 2:528822/90‑1 (MQ=255)
tCCCCATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACCTGCCACGCGCGATTCa < 1:500612/90‑1 (MQ=255)
cATCACGCGCCCCCAGCGGGTTTCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACCTGCCACGCGCGATTCAACGc < 2:230699/90‑1 (MQ=255)
cATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACCTGCCACGCGCGATTCAACGc < 2:114659/90‑1 (MQ=255)
cATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACCTGCCACGCGCGATTCAACGc < 2:548404/90‑1 (MQ=255)
cATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACCTGCCACGCGCGATTCAACGc < 2:289350/90‑1 (MQ=255)
cATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACCTGCCACGCGCGATTCAACGc < 1:50587/90‑1 (MQ=255)
cATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACCTGCCACGCGCGATTCAACGc < 1:197515/90‑1 (MQ=255)
gTTCCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACCTGCCAcgcgc < 1:54909/61‑1 (MQ=255)
|
GCGCGGCGTGGGTAGTTAAATGACAGCGTTGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTTCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACCTGCCACGCGCGATTCAACGC > NZ_CP009273/2818370‑2818518
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 31 ≤ 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
GCGTGGGTAGTTAAATGACAGCGTTGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTTCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACCTGCCACGCGCGATTCAACGCATCTTCATACTGATTCCAGAAAACCACACCG > NZ_CP009273/2818375‑2818549
|
GCGTGGGTAGTTAAA‑GACAGCGTTGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAA > SRR3722109.113593/1‑100 (MQ=60)
tataagagacagCAGCGTTGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCC < SRR3722109.267701/88‑1 (MQ=60)
GACAGCGTTGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTC < SRR3722109.37683/100‑1 (MQ=60)
AGCGTTGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCAT < SRR3722109.65444/100‑1 (MQ=60)
TTGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACAC < SRR3722109.321344/100‑1 (MQ=60)
TTGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACAC < SRR3722109.457084/100‑1 (MQ=60)
TGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACC < SRR3722109.108792/100‑1 (MQ=60)
TACCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACC < SRR3722109.467546/100‑1 (MQ=60)
GCGCATCGAGGATGCGAGTTTTCCCCATCCCGCCCCCCCAGCGGGTTCCACCGCCGATAACCCCGACGATAATTTCCGGCGGTACTCCATACACCTGCCA < SRR3722109.429531/100‑1 (MQ=60)
agatgtgtataagagacaGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACCTGCCACGCGCGATTCAACGC < SRR3722109.55564/82‑1 (MQ=60)
TCCCCATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACCTGCCACGCGCGATTCAACGCATCTTC < SRR3722109.508167/100‑1 (MQ=60)
CATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACCTGCCACGCGCGATTCAACGCATCTTCATAC < SRR3722109.199923/100‑1 (MQ=60)
CATCACGCGCCCCCAGCGGGTTCCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACCTGCCACGCGCGATTCAACGCATCTTCATAC < SRR3722109.51182/100‑1 (MQ=60)
TCCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACCTGCCACGCGCGATTCAACGCATCTTCATACTGATTCCAGAAAACCACACCG < SRR3722109.208197/100‑1 (MQ=60)
|
GCGTGGGTAGTTAAATGACAGCGTTGCCAGCGCATCGAGGATGCGAGTTTTCCCCATCACGCGCCCCCAGCGGGTTTCAACGCCGATAATCCCGACGATAATTTCCGGCGGTACTCCATACACCTGCCACGCGCGATTCAACGCATCTTCATACTGATTCCAGAAAACCACACCG > NZ_CP009273/2818375‑2818549
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
