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 |
|
A5 F8 I0 R1
|
43 |
62.4 |
4721813 |
98.4% |
4646263 |
62.0 |
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%
| 186.6
/ NA
| 62 | 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 (29/33); total (29/33) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
CAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTT > W3110S.gb/2866043‑2866175
|
cAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAAt < 1:755501/70‑1 (MQ=255)
cacacGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTcta > 1:3909500/1‑71 (MQ=255)
cacacGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTcta > 1:1758527/1‑71 (MQ=255)
acacGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctac > 1:3444684/1‑71 (MQ=255)
acacGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctac < 1:718923/71‑1 (MQ=255)
acacGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTcta > 1:4357423/1‑70 (MQ=255)
cacGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctac > 1:2395981/1‑70 (MQ=255)
cacGCTGTGTGGCCCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctact < 1:1496923/71‑1 (MQ=255)
acGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctacta < 1:4550083/71‑1 (MQ=255)
gCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACT‑GGTTCCAATTCTACTaa > 1:3226843/1‑69 (MQ=255)
gCTATGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAg < 1:2924135/71‑1 (MQ=255)
tgtgGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGc > 1:3030168/1‑69 (MQ=255)
tgtgGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGc > 1:3024858/1‑69 (MQ=255)
tgGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCt > 1:2172242/1‑69 (MQ=255)
gCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTc > 1:569183/1‑71 (MQ=255)
gCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTc > 1:465771/1‑71 (MQ=255)
cTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaa < 1:2525093/71‑1 (MQ=255)
gATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAAc > 1:1329186/1‑71 (MQ=255)
aTAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTc < 1:4376933/46‑1 (MQ=255)
aTAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTc < 1:1375863/46‑1 (MQ=255)
aTAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAAcc < 1:4302082/71‑1 (MQ=255)
tAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctact < 1:2395815/49‑1 (MQ=255)
tAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctact < 1:321482/49‑1 (MQ=255)
tAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctact < 1:1735241/49‑1 (MQ=255)
aaCAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAAtt > 1:2002503/1‑43 (MQ=255)
aaCAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAAtt > 1:4380505/1‑43 (MQ=255)
aaCAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGc > 1:2319658/1‑53 (MQ=255)
aCAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTc < 1:4584652/43‑1 (MQ=255)
aCAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCa < 1:2153535/71‑1 (MQ=255)
aGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCaa > 1:605474/1‑70 (MQ=255)
ttCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCt < 1:2041985/50‑1 (MQ=255)
ctctTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaaa < 1:3135570/58‑1 (MQ=255)
ctctTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaaa < 1:896346/58‑1 (MQ=255)
tctTCGGCCAAATCGTTATCACTGGGTTCCAATTctact < 1:3811532/39‑1 (MQ=255)
tctTCGGCCAAATCGTTATCACTGGGTTCCAATTctact < 1:2754136/39‑1 (MQ=255)
tctTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaaaa > 1:2245634/1‑58 (MQ=255)
tctTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTc < 1:1129806/62‑1 (MQ=255)
ctTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTtc > 1:4719276/1‑71 (MQ=255)
ttCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCtt < 1:4378097/45‑1 (MQ=255)
ttCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTtct > 1:2820734/1‑71 (MQ=255)
tCGGCCAAATCGTTATCACTGGGTTCCAATTctacta > 1:1507333/1‑37 (MQ=255)
tCGGCCAAATCGTTATCACTGGGTTCCAATTctacta > 1:3859748/1‑37 (MQ=255)
cGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGTCCTTTTCGTCAAAAACCTCAACTCCGTtct < 1:3226274/69‑1 (MQ=255)
cGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTtct < 1:4673577/69‑1 (MQ=255)
cGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTtct > 1:4600365/1‑69 (MQ=255)
cGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCtca > 1:3114145/1‑71 (MQ=255)
gCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTc < 1:1018143/56‑1 (MQ=255)
ccAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCtt < 1:791249/40‑1 (MQ=255)
ccAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCtcatca < 1:1555188/71‑1 (MQ=255)
aaaTCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTc > 1:2814334/1‑41 (MQ=255)
aaaTCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTc > 1:1711794/1‑41 (MQ=255)
aaaTCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTc > 1:971515/1‑41 (MQ=255)
aaaTCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACt > 1:2264169/1‑57 (MQ=255)
aaTCGTTATCACTGGGTTCCAATTCTACTAAGGCCtt < 1:1640588/37‑1 (MQ=255)
tCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaaa < 1:4476117/45‑1 (MQ=255)
tCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTc < 1:265173/71‑1 (MQ=255)
cGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTcc > 1:1713901/1‑71 (MQ=255)
aTCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCAt > 1:1768549/1‑71 (MQ=255)
tCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCAt < 1:3181890/70‑1 (MQ=255)
gggtCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCAtt < 1:1285689/68‑1 (MQ=255)
ggTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCAt < 1:3313609/70‑1 (MQ=255)
gTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCAttt < 1:3171206/71‑1 (MQ=255)
|
CAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTT > W3110S.gb/2866043‑2866175
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
