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 I199 R1
|
220 |
57.5 |
3163680 |
97.0% |
3068769 |
86.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
818,875 |
A→G |
N107N (AAT→AAC) |
clsB ← |
cardiolipin synthase ClsB |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 818,875 | 0 | A | G | 97.6%
| 127.7
/ ‑4.2
| 42 | N107N (AAT→AAC) | clsB | cardiolipin synthase ClsB |
| Reads supporting (aligned to +/- strand): ref base A (0/1); new base G (24/17); total (24/18) |
| Fisher's exact test for biased strand distribution p-value = 4.29e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.56e-01 |
TATGCTCGGCGGAGTAATTCAGCCCGCCAATAAAGGCTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACATTGGTGCGCATACCAAAAAGGCGAGGGCGGGGATCGTAGTAGCGGAACACTACGCCAGCTGCCGTCAGTTCATTGACAAACTCAT > NZ_CP009273/818790‑818960
|
tatGCTCGGCGGAGTAATTCAGCCCGCCAATAAAGGCTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTgg > 1:1131911/1‑90 (MQ=255)
tatGCTCGGCGGAGTAATTCAGCCCGCCAATAAAGGCTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTgg > 2:1298141/1‑90 (MQ=255)
tatGCTCGGCGGAGTAATTCAGCCCGCCAATAAAGGCTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTgg > 1:1030786/1‑90 (MQ=255)
tatGCTCGGCGGAGTAATTCAGCCCGCCAATAAAGGCTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTgg > 1:689666/1‑90 (MQ=255)
tatGCTCGGCGGAGTAATTCAGCCCGCCAATAAAGGCTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTgg > 1:427794/1‑90 (MQ=255)
taggCTCGGGGGAGTAATTCAGCCCGCCAATAAAGGCTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTgg < 2:1383870/87‑1 (MQ=255)
gCTCGGCGGAGTAATTCAGCCCGCCAATAAAGGCTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTgc > 1:664327/1‑90 (MQ=255)
tCGGCGGAGTAATTCAGCCCGCCAATAAAGGCTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTgcgc < 1:1298141/90‑1 (MQ=255)
cggcggAGTAATTCAGCCCGCCAATAAAGGCTATACGCGCGTCGGTGACCAAAATTTTGCGATGCATCCGGCGAAACACGGTGGGGCGCa > 1:1425570/1‑90 (MQ=255)
cggcggAGTAATTCAGCCCGCCAATAAAGGCTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTGCGCa > 1:880406/1‑90 (MQ=255)
cggcggAGTAATTCAGCCCGCCAATAAAGGCTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTGCGCa > 2:995778/1‑90 (MQ=255)
cggcggAGTAATTCAGCCCGCCAATAAAGGCTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTGCGCa > 1:1072579/1‑90 (MQ=255)
gggggAGTAATTCAGCCCGCCAATAAAGGCTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTGCGCAt < 1:660220/87‑1 (MQ=255)
aGCCCGCCAATAAAGGCTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTGCGCATACCAAAAAGGCGa < 2:1030786/90‑1 (MQ=255)
aGCCCGCCAATAAAGGCTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTGCGCATACCAAAAAGGCGa < 1:1075249/90‑1 (MQ=255)
ccAATAAAGGCTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTGCGCATACCAAAAAGGCGAGGGCgg < 1:259910/90‑1 (MQ=255)
aaaGGCTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTGCGCATACCAAAAAGGCGAGGGCGGGGATc < 2:177519/90‑1 (MQ=255)
ggCTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTGCGCATACCAAAAAGGCGAGGGCGGGGATCgta < 1:569765/90‑1 (MQ=255)
cTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTgcgc > 2:973781/1‑59 (MQ=255)
cTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTgcgc < 1:973781/59‑1 (MQ=255)
cTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTGCGCATACCAAAAAGGCGa > 1:1241798/1‑74 (MQ=255)
cTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTGCGCATACCAAAAAGGCGa < 2:1241798/74‑1 (MQ=255)
cTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACATTGGTGCGCATACCAAAAAGGCGAGGGCGGGGATCgtagt < 2:380619/90‑1 (MQ=255)
tataCGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTGCGCATACCAAAAAGGCGAGGGCGGGGATCgtagta > 1:77709/1‑90 (MQ=255)
ataCGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTGCGCATACCAAAAAGGCGAGGGCGGGGATCGtagtag > 1:509316/1‑90 (MQ=255)
ataCGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTGCGCATACCAAAAAGGCGAGGGCGGGGATCGtagtag > 2:659873/1‑90 (MQ=255)
ataCGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTGCGCATACCAAAAAGGCGAGGGCGGGGATCGtagtag > 1:1202697/1‑90 (MQ=255)
taCGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTGCGCATACCAAAAAGGCGAGGGCGGGGATCGTAGTAGc > 2:482829/1‑90 (MQ=255)
aCGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTGCGCATACCAAAAAGGCGAGGGCgg > 2:27197/1‑76 (MQ=255)
aCGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTGCGCATACCAAAAAGGCGAGGGCgg < 1:27197/76‑1 (MQ=255)
gcgcgTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTGCGCATACCAAAAAGGCGAGGGCGGGGATCGTAGTAGCGGa < 2:1150355/90‑1 (MQ=255)
gcgcgTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTGCGCATACCAAAAAGGCGAGGGCGGGGATCGTAGTAGCGGa < 2:1347033/90‑1 (MQ=255)
gcgTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTGCGCATACCAAAAAGGCGa < 2:163419/66‑1 (MQ=255)
gcgTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTGCGCATACCAAAAAGGCGa > 1:163419/1‑66 (MQ=255)
gcgTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTGCGCATACCAAAAAGGCGAGGGCGGGGATCGTAGTAGc < 2:1323288/85‑1 (MQ=255)
gcgTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTGCGCATACCAAAAAGGCGAGGGCGGGGATCGTAGTAGc > 1:1323288/1‑85 (MQ=255)
cgTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTGCGCATACCAAAAAGGCGAGGGCGGGGATCGTAGTAGCGGAaca < 2:1131911/90‑1 (MQ=255)
gCGATGCATCCGGCGAAACACGTTGGTGCGCATACCAAAAAGGCGAGGGCGGGGATCGTAGTAGCGGAACACTACGCCAGCTGCCGTCAg > 2:1031013/1‑90 (MQ=255)
gCGATGCATCCGGCGAAACACGTTGGTGCGCATACCAAAAAGGCGAGGGCGGGGATCGTAGTAGCGGAACACTACGCCAGCTGCCGTCAg > 1:348927/1‑90 (MQ=255)
cATCCGGCGAAACACGTTGGTGCGCATACCAAAAAGGCGAGGGCGGGGATCGTAGTAGCGGAACACTACGCCAGCTGCCGTCAGTTCAtt > 1:925550/1‑90 (MQ=255)
aaaCACGTTGGTGCGCATACCAAAAAGGCGAGGGCGGGGATCGTAGTAGCGGAACACTACGCCAGCTGCCGTCAGTTCATTGACAAACTc < 2:1202697/90‑1 (MQ=255)
acacGTTGGTGCGCATACCAAAAAGGCGAGGGCGGGGATCGTAGTAGCGGAACACTACGCCAGCTGCCGTCAGTTCATTGACAAACTCAt > 1:545125/1‑90 (MQ=255)
|
TATGCTCGGCGGAGTAATTCAGCCCGCCAATAAAGGCTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACATTGGTGCGCATACCAAAAAGGCGAGGGCGGGGATCGTAGTAGCGGAACACTACGCCAGCTGCCGTCAGTTCATTGACAAACTCAT > NZ_CP009273/818790‑818960
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ 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
TAGCTGGACATATGCTCGGCGGAGTAATTCAGCCCGCCAATAAAGGCTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACATTGGTGCGCATACCAAAAAGGCGAGGGCGGGGATCGTAGTAGCGGAACACTACGCCAGCTGCCGTCAGTTCATTGACAAACTCATCGCTGAGATC > NZ_CP009273/818780‑818970
|
TAGCTGGACATATGCTCGGCGGAGTAATTCAGCCCGCCAATAAAGGCTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGG > SRR3722078.1046089/1‑100 (MQ=60)
TAGCTGGACATATGCTCGGCGGAGTAATTCAGCCCGCCAATAAAGGCTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGG > SRR3722078.1149244/1‑100 (MQ=60)
TAGCTGGACATATGCTCGGCGGAGTAATTCAGCCCGCCAATAAAGGCTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGG > SRR3722078.697831/1‑100 (MQ=60)
TAGCTGGACATATGCTCGGCGGAGTAATTCAGCCCGCCAATAAAGGCTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGG > SRR3722078.432948/1‑100 (MQ=60)
CTGGACATATGCTCGGCGGAGTAATTCAGCCCGCCAATAAAGGCTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTGC > SRR3722078.671934/1‑100 (MQ=60)
GACATATGCTCGGCGGAGTAATTCAGCCCGCCAATAAAGGCTATACGCGCGTCGGTGACCAAAATTTTGCGATGCATCCGGCGAAACACGGTGGGGCGCA > SRR3722078.1448739/1‑100 (MQ=60)
GACATATGCTCGGCGGAGTAATTCAGCCCGCCAATAAAGGCTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTGCGCA > SRR3722078.1088771/1‑100 (MQ=60)
GACATATGCTCGGCGGAGTAATTCAGCCCGCCAATAAAGGCTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTGCGCA > SRR3722078.892244/1‑100 (MQ=60)
CATATGCTCGGCGGAGTAATTCAGCCCGCCAATAAAGGCTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTGCGCctg > SRR3722078.993657/1‑97 (MQ=60)
tcagatgtgtataagagacaGCCAATAAAGGCTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTGCGCATACCAAAAA < SRR3722078.987751/80‑1 (MQ=60)
gcggcggaatattcccGCCCGCCAATAAAGGCTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTGCGCATACCAAAAA < SRR3722078.70088/84‑1 (MQ=60)
ccgggggatTAATTCAGCCCGCCAATAAAGGCTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTGCGCATACCAAAAA < SRR3722078.1318810/91‑1 (MQ=60)
GGGGGAGTAATTCAGCCCGCCAATAAAGGCTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTGCGCATACCAAAAAGG < SRR3722078.667776/100‑1 (MQ=60)
ccCCCGCCAATAAAGGCTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTGCGCATACCAAAAAGGCGAGGGCGGGGAT < SRR3722078.1091495/98‑1 (MQ=60)
acagTAAAGGCTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTGCGCATACCAAAAAGGCGAGGGCGGGGATCGTAGT < SRR3722078.27533/96‑1 (MQ=60)
CCAATAAAGGCTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTGCGCATACCAAAAAGGCGAGGGCGGGGATCtgtct > SRR3722078.1261415/1‑95 (MQ=60)
CCAATAAAGGCTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTGCGCATACCAAAAAGGCGAGGGCGGGGATCGTAGT < SRR3722078.263088/100‑1 (MQ=60)
CAATAAAGGCTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTGCGCATACCAAAAAGGCGAGGGCGGGGATCGTAGTA > SRR3722078.78628/1‑100 (MQ=60)
AATAAAGGCTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTGCGCATACCAAAAAGGCGAGGGCGGGGATCGTAGTAG > SRR3722078.515347/1‑100 (MQ=60)
AATAAAGGCTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTGCGCATACCAAAAAGGCGAGGGCGGGGATCGTAGTAG > SRR3722078.1221559/1‑100 (MQ=60)
GGCTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTGCGCATACCAAAAAGGCGAGGGCGGGGATCtgtctcttataca > SRR3722078.165322/1‑87 (MQ=60)
GGCTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTGCGCATACCAAAAAGGCGAGGGCGGGGATCGTAGTAGCGGAAC < SRR3722078.576439/100‑1 (MQ=60)
GGCTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTGCGCATACCAAAAAGGCGAGGGCGGGGATCGTAGTAGCGGAAC > SRR3722078.1344441/1‑100 (MQ=60)
acgaccgccatcgtcggcagcgtcagatgtgtataagagacaGAAACACATTGGTGCGCATACCAAAAAGGCGAGGGCGGGGATCGTAGTAGCGGAACAC < SRR3722078.1382133/58‑1 (MQ=60)
CCACAATTTTGCGATGCATCCGGCGAAACACGTTGGTGCGCATACCAAAAAGGCGAGGGCGGGGATCGTAGTAGCGGAACACTACGCCAGCTGCCGTCAG > SRR3722078.353203/1‑100 (MQ=60)
TTTTGCGATGCATCCGGCGAAACACGTTGGTGCGCATACCAAAAAGGCGAGGGCGGGGATCGTAGTAGCGGAACACTACGCCAGCTGCCGTCAGTTCATT > SRR3722078.938257/1‑100 (MQ=60)
GCATCCGGCGAAACACGTTGGTGCGCATACCAAAAAGGCGAGGGCGGGGATCGTAGTAGCGGAACACTACGCCAGCTGCCnnnnnnnnnnnnnnnnnnnn > SRR3722078.1480812/1‑80 (MQ=60)
ATCCGGCGAAACACGTTGGTGCGCATACCAAAAAGGCGAGGGCGGGGATCGTAGTAGCGGAACACTACGCCAGCTGCCGTCAGTTCATTGACAAACTCAT > SRR3722078.551562/1‑100 (MQ=60)
CGGCGAAACACGTTGGTGCGCATACCAAAAAGGCGAGGGCGGGGATCGTAGTAGCGGAACACTACGCCAGCTGCCGTCAGTTCATTGACAAACTCATCGC > SRR3722078.170301/1‑100 (MQ=60)
ACACGTTGGTGCGCATACCAAAAAGGCGAGGGCGGGGATCGTAGTAGCGGctgtctcttatacacatctgacgctgccgacgatggcgggcgtgtagatc > SRR3722078.610119/1‑50 (MQ=60)
ACACGTTGGTGCGCATACCAAAAAGGCGAGGGCGGGGATCGTAGTAGCGGAACACTACGCCAGCTGCCGTCAGTTCATTGACAAACTCATCGCTGAGATC > SRR3722078.121594/1‑100 (MQ=60)
|
TAGCTGGACATATGCTCGGCGGAGTAATTCAGCCCGCCAATAAAGGCTATACGCGCGTCGATCACCACAATTTTGCGATGCATCCGGCGAAACACATTGGTGCGCATACCAAAAAGGCGAGGGCGGGGATCGTAGTAGCGGAACACTACGCCAGCTGCCGTCAGTTCATTGACAAACTCATCGCTGAGATC > NZ_CP009273/818780‑818970
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
