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 F17 I0 R2
|
276 |
45.3 |
3729697 |
93.0% |
3468618 |
60.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
2,866,110 |
T→A |
100% |
intergenic (‑20/+160) |
rpoS ← / ← nlpD |
RNA polymerase, sigma S (sigma 38) factor/predicted outer membrane lipoprotein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,866,110 | 0 | T | A | 100.0%
| 135.7
/ NA
| 46 | intergenic (‑20/+160) | rpoS/nlpD | RNA polymerase, sigma S (sigma 38) factor/predicted outer membrane lipoprotein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base A (29/17); total (29/17) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
GCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCA > W3110S.gb/2866051‑2866172
|
gCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctacta > 1:573286/1‑69 (MQ=255)
ggCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTc < 1:2529326/57‑1 (MQ=255)
gCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCtt < 1:2846516/68‑1 (MQ=255)
gCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCtt < 1:3073999/68‑1 (MQ=255)
gCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCtt < 1:2338359/68‑1 (MQ=255)
gCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCtt < 1:1663990/68‑1 (MQ=255)
cTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCtt < 1:3323825/67‑1 (MQ=255)
cccTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTc < 1:698175/68‑1 (MQ=255)
gCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCa > 1:717408/1‑68 (MQ=255)
aTAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaaa < 1:1261901/68‑1 (MQ=255)
aTAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaaa < 1:1981169/68‑1 (MQ=255)
aTAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaaa < 1:1497691/68‑1 (MQ=255)
aTAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaa < 1:1415883/67‑1 (MQ=255)
aaCAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTgtact < 1:1590064/48‑1 (MQ=255)
aaCAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctact < 1:507309/48‑1 (MQ=255)
aaCAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCtt < 1:1180468/56‑1 (MQ=255)
aGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTc < 1:11184/68‑1 (MQ=255)
aGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTc < 1:1520436/68‑1 (MQ=255)
tCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTc < 1:924008/38‑1 (MQ=255)
tCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTc > 1:2345257/1‑65 (MQ=255)
tCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTc > 1:1566870/1‑65 (MQ=255)
tCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTc > 1:2980860/1‑65 (MQ=255)
ccTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTc > 1:402254/1‑69 (MQ=255)
ccTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTc > 1:3194311/1‑69 (MQ=255)
ccTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTc > 1:3044082/1‑69 (MQ=255)
ccTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGACAAAAACCTCAACTc > 1:2530173/1‑69 (MQ=255)
cGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaaaa > 1:968030/1‑54 (MQ=255)
cGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaaaa > 1:2792774/1‑54 (MQ=255)
cGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaa > 1:3037408/1‑52 (MQ=255)
cGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTtct > 1:1696644/1‑69 (MQ=255)
aTCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGtt > 1:708426/1‑60 (MQ=255)
aTCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGtt > 1:1895393/1‑60 (MQ=255)
aTCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGtt > 1:1919519/1‑60 (MQ=255)
cGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAAt > 1:2473129/1‑68 (MQ=255)
aTCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGc > 1:1892803/1‑69 (MQ=255)
aCTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTc > 1:3680279/1‑42 (MQ=255)
aCTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTc > 1:1879029/1‑42 (MQ=255)
aCTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTc > 1:519081/1‑42 (MQ=255)
aCTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTc > 1:2920982/1‑42 (MQ=255)
aCTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTc > 1:1930381/1‑42 (MQ=255)
aCTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTc > 1:2808573/1‑42 (MQ=255)
gggTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTc > 1:3197215/1‑69 (MQ=255)
ggTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCa > 1:1893654/1‑69 (MQ=255)
ggTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCa > 1:2605511/1‑69 (MQ=255)
ggTTCCAATTCTACTAAGGCCTTTTAGTCAAAAACCTCa > 1:1889296/1‑39 (MQ=38)
gTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCa > 1:3329508/1‑68 (MQ=255)
|
GCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCA > W3110S.gb/2866051‑2866172
|
| 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
