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 |
3,786,991 |
T→C |
D18G (GAT→GGT) |
yibB ← |
protein YibB |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,786,991 | 0 | T | C | 93.3%
| 38.4
/ ‑3.5
| 15 | D18G (GAT→GGT) | yibB | protein YibB |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base C (6/8); total (6/9) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TTTCAAGTGCGGCCAGACGCTCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAATCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCATTACTAATAAGACCATTAATATAAAAAAAGA > NZ_CP009273/3786902‑3787073
|
tttCAAGTGCGGCCAGACGCTCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAAt < 1:529414/90‑1 (MQ=255)
tCAAGTGCGGCCAGACGCTCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAAccc < 2:536257/90‑1 (MQ=255)
aaGTGCGGCCAGACGCTCAAAGTAACTAAAATAAACATTAACTGAACGAGCCCGTTTTTCCCGGAAACCTTTATTAGCAGTCCAATcccc < 1:511137/90‑1 (MQ=255)
ggCCAGACGCTCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTAcc < 1:377482/90‑1 (MQ=255)
ggCCAGACGCTCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTAcc < 1:588760/90‑1 (MQ=255)
tCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCaaaa > 1:586014/1‑90 (MQ=255)
aCTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGt > 1:419349/1‑90 (MQ=255)
cTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTg < 1:315252/90‑1 (MQ=255)
aaaaTAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGAt < 1:177974/90‑1 (MQ=255)
aCATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCa > 2:95855/1‑78 (MQ=255)
aCATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCa < 1:95855/78‑1 (MQ=255)
cTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGgatg < 2:407216/90‑1 (MQ=255)
cGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTc < 2:211665/90‑1 (MQ=255)
cGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTc < 1:118058/90‑1 (MQ=255)
aGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCATTACTAATAAGACCATTAATATaaaaaa > 1:17199/1‑90 (MQ=255)
aGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCATTACTAATAAGACCATTAATATAAAAAAAGa > 1:396352/1‑90 (MQ=255)
aGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCATTACTAATAAGACCATTAATATAAAAAAAGa > 1:9729/1‑90 (MQ=255)
|
TTTCAAGTGCGGCCAGACGCTCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAATCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCATTACTAATAAGACCATTAATATAAAAAAAGA > NZ_CP009273/3786902‑3787073
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 34 ≤ 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
CATCTCATTTTCAAGTGCGGCCAGACGCTCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAATCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCATTACTAATAAGACCATTAATATAAAAAAAGA > NZ_CP009273/3786894‑3787073
|
CATCTCATTTTCAAGTGCGGCCAGACGCTCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCC < SRR3722109.398731/100‑1 (MQ=60)
TTTCAAGTGCGGCCAGACGCTCAAAGTAACTAAAATAAACATCAACTGACCGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACC < SRR3722109.518528/100‑1 (MQ=60)
TTTCAAGTGCGGCCAGACGCTCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAATCCCCTCTACC < SRR3722109.537473/100‑1 (MQ=60)
TTTCAAGTGCGGCCAGACGCTCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACC < SRR3722109.420228/100‑1 (MQ=60)
AAGTGCGGCCAGACGCTCAAAGTAACTAAAATAAACATTAACTGAACGAGCCCGTTTTTCCCGGAAACCTTTATTAGCAGTCCAATCCCCTCTACCAATG < SRR3722109.518879/100‑1 (MQ=60)
GGCCAGACGCTCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAA < SRR3722109.382832/100‑1 (MQ=60)
GGCCAGACGCTCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAA < SRR3722109.597667/100‑1 (MQ=60)
GGCCAGACGCTCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAA > SRR3722109.594888/1‑100 (MQ=60)
GCTCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGT > SRR3722109.425494/1‑100 (MQ=60)
agACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGATAATTG < SRR3722109.97046/98‑1 (MQ=60)
CTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGG < SRR3722109.319402/100‑1 (MQ=60)
AAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTG < SRR3722109.180167/100‑1 (MQ=60)
AACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCctgtctcttatacacatctgacgctgccgacgaatgt > SRR3722109.116424/1‑63 (MQ=60)
CGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCATTACTAATA < SRR3722109.119518/100‑1 (MQ=60)
ACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCATTACTAATAAGACCATTAATATAAAAAA > SRR3722109.17423/1‑100 (MQ=60)
CTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCATTACTAATAAGACCATTAATATAAAAAAAGA > SRR3722109.402054/1‑100 (MQ=60)
CTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCATTACTAATAAGACCATTAATATAAAAAAAGA > SRR3722109.9863/1‑100 (MQ=60)
|
CATCTCATTTTCAAGTGCGGCCAGACGCTCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAATCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCATTACTAATAAGACCATTAATATAAAAAAAGA > NZ_CP009273/3786894‑3787073
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
