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 F1 I0 R2
|
201 |
99.6 |
7939938 |
96.9% |
7693799 |
60.1 |
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%
| 225.6
/ NA
| 75 | 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 (49/26); total (49/26) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
CAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCA > W3110S.gb/2866043‑2866172
|
cAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAAt > 1:1467093/1‑70 (MQ=255)
cAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAAt > 1:3294240/1‑70 (MQ=255)
aaCACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTc > 1:6161166/1‑71 (MQ=255)
acacacGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTc > 1:1557227/1‑70 (MQ=255)
cacacGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTcta > 1:3526774/1‑71 (MQ=255)
acacGCTGTGTGGCTTCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctac > 1:4265064/1‑71 (MQ=255)
cacGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctact < 1:4004431/71‑1 (MQ=255)
acGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctacta < 1:2660604/71‑1 (MQ=255)
cGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTaa < 1:3703494/71‑1 (MQ=255)
gCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAg > 1:1102697/1‑71 (MQ=255)
cTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAgg > 1:4143356/1‑71 (MQ=255)
gtgtgGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctact < 1:4532169/65‑1 (MQ=255)
tgtgGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCt > 1:7363272/1‑71 (MQ=255)
tgGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCttt < 1:6849699/71‑1 (MQ=255)
tgGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCttt < 1:4808620/71‑1 (MQ=255)
gCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTc > 1:7662683/1‑71 (MQ=255)
cTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTc > 1:1921083/1‑70 (MQ=255)
ccTGCGATAACAGTTCGTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTc > 1:3463790/1‑70 (MQ=255)
ccTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTc < 1:1082128/70‑1 (MQ=255)
ccTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTc > 1:1353357/1‑70 (MQ=255)
ccTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTc > 1:5147716/1‑70 (MQ=255)
ttcGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGt > 1:845939/3‑67 (MQ=255)
cGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTaa > 1:1724406/1‑54 (MQ=255)
cGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTaa > 1:3496009/1‑54 (MQ=255)
cGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGt > 1:5939726/1‑65 (MQ=255)
cGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaaa < 1:631465/70‑1 (MQ=255)
cGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaa < 1:4363174/69‑1 (MQ=255)
gATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctact < 1:6966330/51‑1 (MQ=255)
gATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAAc > 1:4093546/1‑71 (MQ=255)
gATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAAc > 1:2466056/1‑71 (MQ=255)
aTAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCtt < 1:2504981/58‑1 (MQ=255)
aCAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctac > 1:7269270/1‑46 (MQ=255)
aGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTcta > 1:2472497/1‑43 (MQ=255)
tttCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACt > 1:583574/2‑71 (MQ=255)
ccTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTcc < 1:6347875/70‑1 (MQ=255)
ccTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCg > 1:4788266/1‑71 (MQ=255)
tctTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCg < 1:924962/69‑1 (MQ=255)
tctTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTAGTCAAAAACCTCAACTCCGtt > 1:2173769/1‑71 (MQ=255)
ctTCGGCCAAATCGTTATCACTGGGTTCCAATTcta < 1:5845500/36‑1 (MQ=255)
ctTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCttt < 1:3891901/47‑1 (MQ=255)
ctTCCGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGt > 1:3763560/1‑69 (MQ=255)
ttCGGCCAAATCGTTATCACTGGGTTCCAATTcta > 1:4405364/1‑35 (MQ=255)
ttCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaa > 1:3360252/1‑54 (MQ=255)
tCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTtct > 1:4562024/1‑70 (MQ=255)
cGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTc > 1:4814429/1‑46 (MQ=255)
cGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTtc < 1:6661887/68‑1 (MQ=255)
ccAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACt < 1:3637278/59‑1 (MQ=255)
cAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCtcatca > 1:5361987/1‑70 (MQ=255)
aaTCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAAt > 1:6338546/1‑71 (MQ=255)
aTCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTTGTCaaa < 1:11846/45‑1 (MQ=255)
aTCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTtctc > 1:2086484/1‑63 (MQ=255)
tCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAAcc > 1:6899368/1‑48 (MQ=255)
tCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCaa > 1:1804309/1‑52 (MQ=255)
cGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCg > 1:926462/1‑38 (MQ=255)
cGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCg > 1:2098324/1‑38 (MQ=255)
cGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCg > 1:4953469/1‑38 (MQ=255)
cGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCg > 1:4328797/1‑38 (MQ=255)
cGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCg > 1:6188801/1‑38 (MQ=255)
cGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCg > 1:5807845/1‑38 (MQ=255)
cGTTATCACTGGGTTCCAAATCTACTAAGGCCTTTTCg > 1:7061024/1‑38 (MQ=255)
tATCACTGGGTTCCAATTCTACTAAGGCCTTTTCg < 1:3863174/35‑1 (MQ=255)
tATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaaa > 1:2164774/1‑41 (MQ=255)
tATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaaa > 1:1152905/1‑41 (MQ=255)
tATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaaa > 1:5931401/1‑41 (MQ=255)
aTCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCa < 1:402055/70‑1 (MQ=255)
tCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCAt < 1:6032709/70‑1 (MQ=255)
cACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaa > 1:1328935/1‑36 (MQ=255)
cACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaa > 1:610324/1‑36 (MQ=255)
cACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaa > 1:2531377/1‑36 (MQ=255)
aCTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCt < 1:3207015/70‑1 (MQ=255)
cTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTc < 1:6549737/71‑1 (MQ=255)
cTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTc < 1:3439277/71‑1 (MQ=255)
tGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCaaa < 1:3793199/58‑1 (MQ=255)
ggTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCaa > 1:5042871/1‑40 (MQ=255)
ggTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCa < 1:7471427/69‑1 (MQ=255)
|
CAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCA > W3110S.gb/2866043‑2866172
|
| 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
