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 F17 I0 R1
|
87 |
56.5 |
4283937 |
98.6% |
4223961 |
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%
| 184.7
/ 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 (24/38); total (24/38) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
CCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATT > W3110S.gb/2866042‑2866174
|
ccAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAAt > 1:1945258/1‑71 (MQ=255)
cAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAAtt > 1:1377980/1‑71 (MQ=255)
cacacGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAAtt > 1:2581887/1‑68 (MQ=255)
cacacGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTcta < 1:1070653/71‑1 (MQ=255)
cacacGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTcta < 1:1791348/71‑1 (MQ=255)
acacGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctac > 1:1039634/1‑71 (MQ=255)
cacGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctact < 1:3904604/71‑1 (MQ=255)
cacGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctact < 1:3204662/71‑1 (MQ=255)
cacGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctact < 1:3506874/71‑1 (MQ=255)
acGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctacta < 1:33436/71‑1 (MQ=255)
acGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctacta < 1:3806839/71‑1 (MQ=255)
cGCTGTGTGGCTCCCTGCTATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTaa < 1:2623375/71‑1 (MQ=255)
cGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTaa < 1:1271274/71‑1 (MQ=255)
gtgtgGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctact < 1:1758107/65‑1 (MQ=255)
tgGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctact < 1:1950641/62‑1 (MQ=255)
tgGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGGCttt < 1:4207657/71‑1 (MQ=255)
tgGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCttt < 1:257609/71‑1 (MQ=255)
ccTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCttt < 1:3023640/65‑1 (MQ=255)
ccTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGt < 1:3884465/69‑1 (MQ=255)
ccTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCa < 1:4151763/71‑1 (MQ=255)
cTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTc < 1:1319476/69‑1 (MQ=255)
tGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaa > 1:276546/1‑70 (MQ=255)
gCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctacta > 1:2277390/1‑54 (MQ=255)
cGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaaa < 1:717965/70‑1 (MQ=255)
gATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAAc > 1:2628713/1‑71 (MQ=255)
aaCAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAGAAACCt > 1:2074408/1‑70 (MQ=255)
aaCAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCt > 1:3391353/1‑70 (MQ=255)
aCAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTcta > 1:1205299/1‑45 (MQ=255)
aCAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTc < 1:1256860/70‑1 (MQ=255)
aCAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTc > 1:582856/1‑70 (MQ=255)
cAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCaa < 1:685890/71‑1 (MQ=255)
aGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAAc < 1:208877/65‑1 (MQ=255)
gTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaa < 1:4109457/61‑1 (MQ=255)
ttCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAAt < 1:1309939/37‑1 (MQ=255)
ttCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAAt < 1:2711440/37‑1 (MQ=255)
tCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTcc > 1:1654846/1‑71 (MQ=255)
ccTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTc < 1:216968/37‑1 (MQ=255)
tctTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTc < 1:1779939/50‑1 (MQ=255)
ctTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCtttt > 1:283744/1‑48 (MQ=255)
ctTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAAACTCaa > 1:2947843/1‑63 (MQ=255)
tCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTtct > 1:2375374/1‑70 (MQ=255)
cGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCttt < 1:2288655/44‑1 (MQ=255)
cGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaaaa > 1:887662/1‑54 (MQ=255)
ggCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCtca < 1:763453/70‑1 (MQ=255)
ccAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCtcatca < 1:350956/71‑1 (MQ=255)
ccAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCtcatca < 1:357994/71‑1 (MQ=255)
ccAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCtcatca < 1:1344155/71‑1 (MQ=255)
cAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaaaa > 1:2982822/1‑50 (MQ=255)
cAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCtcatca > 1:3775512/1‑70 (MQ=255)
aTCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaaaa > 1:614505/1‑47 (MQ=255)
aTCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGtt > 1:1135384/1‑60 (MQ=255)
aTCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAAtt < 1:571051/71‑1 (MQ=255)
gTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTcc < 1:250798/70‑1 (MQ=255)
gTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTcc < 1:3609945/70‑1 (MQ=255)
ttATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCaa < 1:3935216/49‑1 (MQ=255)
ttATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAAtt < 1:1482582/67‑1 (MQ=255)
tATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaa < 1:3038230/39‑1 (MQ=255)
aTCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCa < 1:1165885/70‑1 (MQ=255)
cACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCa > 1:2612073/1‑68 (MQ=255)
ggTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCa > 1:2184809/1‑39 (MQ=255)
ggTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGt > 1:3090600/1‑46 (MQ=255)
gTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCAtt > 1:19652/1‑70 (MQ=255)
|
CCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATT > W3110S.gb/2866042‑2866174
|
| 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
