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 F3 I0 R2
|
260 |
44.3 |
3360226 |
90.5% |
3041004 |
64.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
4,295,565 |
T→C |
42.9% |
F154F (TTT→TTC) |
nrfE → |
heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfE |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 4,295,565 | 0 | T | C | 42.9%
| 17.8
/ 59.8
| 49 | F154F (TTT→TTC) | nrfE | heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfE |
| Reads supporting (aligned to +/- strand): ref base T (15/13); new base C (8/13); total (23/26) |
| Fisher's exact test for biased strand distribution p-value = 3.88e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GATATTTCCACCAGCAATCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTTCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCGTGGCGCTGGC > W3110S.gb/4295499‑4295627
|
gATATTTCCACCAGCAATCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATc < 1:2845637/71‑1 (MQ=255)
tCCACCAGCAATCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCTGTCTTATCTTCCATCCACCgc > 1:2529614/1‑71 (MQ=255)
tCCACCAGCAATCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCgc > 1:1009521/1‑71 (MQ=255)
tCCACCAGCAATCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCgc > 1:321464/1‑71 (MQ=255)
tCCACCAGCAATCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCgc > 1:2554178/1‑71 (MQ=255)
tCCACCAGCAATCGAAGGCAGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCgc > 1:1683928/1‑71 (MQ=255)
ccaccaGCAATCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCgc < 1:2569755/70‑1 (MQ=255)
ccaccaGCAATCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCgc < 1:1614002/70‑1 (MQ=255)
ccaccaGCAATCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCgc < 1:2311738/70‑1 (MQ=255)
caccaGCAATCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCgc < 1:320250/69‑1 (MQ=255)
gCAATCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTTCATCCACCGCTGCTTTa < 1:2978740/71‑1 (MQ=255)
gCAATCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTTCATCCACCGCTGCTTTa < 1:1653902/71‑1 (MQ=255)
aTCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCttt < 1:560140/67‑1 (MQ=255)
aTCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCttt < 1:473990/67‑1 (MQ=255)
aTCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCttt < 1:3295763/67‑1 (MQ=255)
aTCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCttt < 1:2240349/67‑1 (MQ=255)
gAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTTCATCCACCGCTGCTTTACCTTgg > 1:280916/1‑71 (MQ=255)
cAATCCGATGCTGCAACATCCCGGTCTTATCTTTCATCCACCGCTTCTTTACCTTgg > 1:447195/1‑57 (MQ=255)
cAATCCGATGCTGCAACATCCCGGTCTTATCTTTCATCCACCGCTGCTTTACCTTgg > 1:1776679/1‑57 (MQ=255)
cAATCCGATGCTGCAACATCCCGGTCTTATCTTTCATCCACCGCTGCTTTACCTTgg > 1:31483/1‑57 (MQ=255)
cAATCCGATGCTGCAACATCCCGGTCTTATCTTTCATCCACCGCTGCTTTACCTTgg > 1:3013841/1‑57 (MQ=255)
cAATCCGATGCTGCAACATCCCGGTCTTATCTTTCATCCACCGCTGCTTTACCTTgg > 1:138533/1‑57 (MQ=255)
cAATCCGATGCTGCAACATCCCGGTCTTATCTTTCATCCACCGCTGCTTTACCTTgg > 1:3191969/1‑57 (MQ=255)
cAATCCGATGCTGCAACATCCCGGTCTTATCTTTCATCCACCGCTGCTTTACCTTgg > 1:669813/1‑57 (MQ=255)
cAAACCGATGCTGCAACATCCCGGTCTTATCTTTCATCCACCGCTGCATTa > 1:3319031/1‑51 (MQ=39)
cGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGt < 1:2327093/70‑1 (MQ=255)
cGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGt < 1:122336/70‑1 (MQ=255)
cGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGt < 1:586918/70‑1 (MQ=255)
cGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGt < 1:3171148/70‑1 (MQ=255)
aTGCTGCAACATCCCGGTCTTATCTTTCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAgc > 1:1293685/1‑71 (MQ=255)
aTGCTGCAACATCCCGGTCTTATCTTTCATCCACCGCTGCTTCACCTTGGCTATGGCGGTTTGATGGTAgc > 1:1515587/1‑71 (MQ=255)
cAACATCCCGGTCTTATCTTTCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAg < 1:766684/71‑1 (MQ=255)
cAACATCCCGGTCTTATCTTTCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAg < 1:1925978/71‑1 (MQ=255)
cAACATCCCGGTCTTATCTTTCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAg < 1:1292693/71‑1 (MQ=255)
cAACATCCCGGTCTTATCTTTCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAg < 1:3101199/71‑1 (MQ=255)
cAACATCCCGGTCTTATCTTTCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAg < 1:761506/71‑1 (MQ=255)
cAACATCCCGGTCTTATCTTTCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAg < 1:2532357/71‑1 (MQ=255)
cAACATCCCGGTCTTATCTTTCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAg < 1:2412070/71‑1 (MQ=255)
cAACATCCCGGTCTTATCTTTCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAg < 1:2322400/71‑1 (MQ=255)
cAACATCCCGGTCTTATCTTTCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAg < 1:1907884/71‑1 (MQ=255)
cAACATCCCGGTCTTATCTTTCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAg < 1:2277869/71‑1 (MQ=255)
ttATCTTTCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCGTGGCGCt < 1:1813927/67‑1 (MQ=255)
ttATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCGTGGCGCTGGc > 1:78166/1‑70 (MQ=255)
ttATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCGTGGCGCTGGc > 1:1535114/1‑70 (MQ=255)
ttATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCGTGGCGCTGGc > 1:1166536/1‑70 (MQ=255)
aTCTTTCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATg > 1:3074657/1‑45 (MQ=255)
aTCTTTCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATg > 1:742341/1‑45 (MQ=255)
aTCTTTCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATg > 1:1297226/1‑45 (MQ=255)
aTCTTTCATCCACCGCTGCTTTACATTGGCTATGGCGGTTTGATg > 1:2035059/1‑45 (MQ=255)
|
GATATTTCCACCAGCAATCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTTCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCGTGGCGCTGGC > W3110S.gb/4295499‑4295627
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
