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 |
|
A2 F999 I1 R1
|
226 |
132.7 |
9745491 |
85.7% |
8351885 |
75.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
3,389,812 |
Δ1 bp |
intergenic (‑149/+4151) |
tldD ← / ← cafA |
TldD/CafA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 3,389,811 | 0 | C | . | 100.0%
| 73.5
/ NA
| 27 | intergenic (‑148/+4152) | tldD/cafA | TldD/CafA |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base . (12/15); total (12/15) |
CCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGCCGGCGTAAACGCCTTATCCGACCTACGGTTATGTTCCGTTTGTAGGCCTGATAAGACG > NC_000913/3389736‑3389869
|
ccAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGc < 1:2671662/76‑1 (MQ=255)
aGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGcgg < 2:3800745/76‑3 (MQ=255)
gCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGcggc < 2:3016971/76‑4 (MQ=255)
gCCTACGGTTATGTTCCGGTTTGGAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGcggc < 2:1944798/76‑4 (MQ=255)
cTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGt > 2:836861/1‑76 (MQ=255)
cTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGt < 1:304087/76‑1 (MQ=255)
tACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTa < 2:4782498/76‑1 (MQ=255)
tACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTa < 1:616047/76‑1 (MQ=255)
gaCGGTTATGTTCGGGTTTGGAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTa < 2:272122/75‑1 (MQ=11)
cGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTaaa < 1:607024/76‑1 (MQ=255)
cGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTaaa < 1:2925682/76‑1 (MQ=255)
ggTTATGTTCTGGTTTGTGGGCCTGATAAGACGCACAGCGTGGCGTCAGGCAACGGCTGTCGGATG‑CGGCGTAAAc < 2:2276030/76‑1 (MQ=11)
ggTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTGAAc > 1:3348254/1‑76 (MQ=11)
ggTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAAc < 1:1365262/76‑1 (MQ=255)
ggTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGGCGGGTG‑CGGCGGAAAc > 1:2518525/1‑76 (MQ=11)
ggTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGGCGGATG‑CGGCGGAAAc > 1:2907340/1‑76 (MQ=11)
gTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGGCGGGTG‑GGGCGTAAAcc > 2:1799066/1‑75 (MQ=11)
ttATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGGCGGATG‑CGGCGTAAACGc > 2:2838897/1‑76 (MQ=11)
taggTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGcc < 1:2151783/73‑1 (MQ=11)
tATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGcc < 1:2873606/76‑1 (MQ=255)
tATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGcc > 1:2785777/1‑76 (MQ=255)
tATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGcc < 2:3512195/76‑1 (MQ=255)
tATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGGCGGGTG‑CGGCGTAAACGcc > 1:2378333/1‑76 (MQ=11)
aTGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGGCGGGTG‑CGGCGGAAACGCCt > 1:2629077/1‑76 (MQ=11)
tGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGGCGGATG‑CGGCGGAAACGccct > 1:2929543/1‑74 (MQ=11)
tCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGCCTTATc < 1:2774926/76‑1 (MQ=255)
tCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGCCTTATc < 1:1027279/76‑1 (MQ=255)
ccGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGCCTTATcc < 1:836861/76‑1 (MQ=12)
ccGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGCCTTATcc > 1:1545416/1‑76 (MQ=9)
cGGTTTGTAGGCCTGATAAGGCGCCCAGCGTCGCATCAGGCACCGTCTGTCGGATG‑CGGCGTAAACGCCTTATCCg < 2:2910844/76‑1 (MQ=11)
ggCAACGGCTGTCGGACG‑CGGCGGAAACGCCCTATCCGGCCTACGGGTATGTTTCCTTTTGAGGCCTTGTAAGaac > 1:3544425/1‑74 (MQ=2)
|
CCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGCCGGCGTAAACGCCTTATCCGACCTACGGTTATGTTCCGTTTGTAGGCCTGATAAGACG > NC_000913/3389736‑3389869
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 6 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
