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 |
|
A6 F21 I0 R1
|
2169 |
63.0 |
3952800 |
76.2% |
3012033 |
62.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,837,480 |
C→G |
6.0% |
L313L (CTG→CTC) |
nlpD ← |
predicted outer membrane lipoprotein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,837,480 | 0 | C | G | 6.0%
| 199.4
/ 2.6
| 66 | L313L (CTG→CTC) | nlpD | predicted outer membrane lipoprotein |
| Reads supporting (aligned to +/- strand): ref base C (23/39); new base G (2/2); total (25/41) |
| Fisher's exact test for biased strand distribution p-value = 6.30e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.09e-01 |
TTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCTGCGGTCGCGATAATTGC > minE/1837411‑1837548
|
ttCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCa < 1:1513270/71‑1 (MQ=255)
ttCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCa < 1:2780036/71‑1 (MQ=255)
ggACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATATTCAGATTa < 1:2477886/71‑1 (MQ=255)
gACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTAc < 1:1708500/71‑1 (MQ=255)
aGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTa < 1:2449955/71‑1 (MQ=255)
gCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAg > 1:3641026/1‑71 (MQ=255)
cATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACAGTAGc > 1:1810632/1‑71 (MQ=255)
atcgtgtCATTATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACCGTAGcc < 1:287334/68‑1 (MQ=255)
gtgtCATTATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTATAATCATGATGAGATTACCGTAGCcacg < 1:83117/71‑1 (MQ=255)
tgtCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTAc < 1:1774504/60‑1 (MQ=255)
tcattATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACCGTAGCCACGCAg > 1:2101558/4‑71 (MQ=255)
tCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTa < 1:3163641/57‑1 (MQ=255)
tCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCa < 1:2246373/70‑1 (MQ=255)
tCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCa > 1:670465/1‑70 (MQ=255)
tATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACCGTAGCCACGCAgctgg > 1:288756/1‑68 (MQ=255)
aTGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCa > 1:3081708/1‑47 (MQ=255)
tGGGCGTAGGCACTCAGGTAATCATCATTATGTTTTATGATAATCAGATTACCg < 1:1727758/54‑1 (MQ=255)
tGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGtt < 1:750420/71‑1 (MQ=255)
tGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGt < 1:3286115/70‑1 (MQ=255)
gggCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTAcc > 1:2829722/1‑52 (MQ=255)
ggCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTa < 1:3128388/70‑1 (MQ=255)
ggCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTa < 1:2046195/70‑1 (MQ=255)
ggCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTAc < 1:687821/71‑1 (MQ=255)
ggCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTAc < 1:833221/71‑1 (MQ=255)
gCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTAc > 1:2730153/1‑70 (MQ=255)
cGTAGGCACTCATGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTAc > 1:1820492/1‑69 (MQ=255)
ggCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGc > 1:2462040/1‑69 (MQ=255)
gCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATa < 1:1055642/71‑1 (MQ=255)
gCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATa < 1:1534082/71‑1 (MQ=255)
aCTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGt < 1:1516067/44‑1 (MQ=255)
aCTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGt < 1:2787297/59‑1 (MQ=255)
aCTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATaaa < 1:2676144/71‑1 (MQ=255)
tCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATaa < 1:516533/68‑1 (MQ=255)
tCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAaac > 1:3068424/1‑70 (MQ=255)
aGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAaacaac > 1:378996/1‑71 (MQ=255)
aGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAaacaa < 1:1070597/70‑1 (MQ=255)
aGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAaaca < 1:1767053/69‑1 (MQ=255)
aGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAaaca < 1:75407/69‑1 (MQ=255)
tAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAaac < 1:945665/65‑1 (MQ=255)
aaTCATCATTATGTTTGATGATAATCAGATTACCGTAGc < 1:2715970/39‑1 (MQ=255)
aaTCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCgg > 1:2244393/1‑71 (MQ=255)
aaTCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCgg > 1:1478642/1‑71 (MQ=255)
aaTCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCgg > 1:1665630/1‑71 (MQ=255)
atcatcATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAaacaa < 1:3049118/65‑1 (MQ=255)
atcatcATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCgg < 1:3259269/70‑1 (MQ=255)
tcatcaTTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGt < 1:2468349/49‑1 (MQ=255)
catcatTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCGGCCa > 1:678726/1‑71 (MQ=255)
atcatTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGt > 1:2459048/1‑47 (MQ=255)
atcatTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAAcgcg > 1:1814366/1‑66 (MQ=255)
tcatTATGTTTGATGATAATCAGATTACCGTAGCCGCGCa < 1:1202875/40‑1 (MQ=255)
catTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCt > 1:1103903/1‑71 (MQ=255)
atTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCt < 1:1718874/70‑1 (MQ=255)
tATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCTGCg > 1:1840381/1‑71 (MQ=255)
aTGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAaacaa > 1:1266913/1‑56 (MQ=255)
tGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAaacaac > 1:3198838/1‑56 (MQ=255)
tGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCTGCGGt < 1:2908566/71‑1 (MQ=255)
tGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCTGCGGt < 1:2668504/71‑1 (MQ=255)
gTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCTGCGGTc > 1:3164968/1‑71 (MQ=255)
tgatgaTAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCTGCGGTcgc < 1:537095/70‑1 (MQ=255)
tAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCTGCGGTCGCGATAAtt < 1:1713799/71‑1 (MQ=255)
tAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCTGCGGTCGCGATAAtt < 1:303170/71‑1 (MQ=255)
aaTCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCTGCGGTcgc > 1:1704941/1‑63 (MQ=255)
aaTCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCTGCGGTcgc > 1:695273/1‑63 (MQ=255)
aTCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCTGCGGTCGCGATAATTGc < 1:988729/71‑1 (MQ=255)
aTCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCTGCGGTCGCGATAATTGc < 1:1365355/71‑1 (MQ=255)
tCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCTGCg < 1:3912845/56‑1 (MQ=255)
|
TTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCTGCGGTCGCGATAATTGC > minE/1837411‑1837548
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
