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 F3 I0 R1
|
43 |
41.2 |
3165159 |
98.4% |
3114516 |
61.0 |
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%
| 134.1
/ NA
| 43 | 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 (20/23); total (20/23) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
CAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTA > W3110S.gb/2866043‑2866176
|
cAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAAtt > 1:2161576/1‑71 (MQ=255)
cAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAAt < 1:1889033/70‑1 (MQ=255)
cAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAAt > 1:2486753/1‑70 (MQ=255)
aaCACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTc < 1:1883764/71‑1 (MQ=255)
acacacGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTc < 1:3027283/70‑1 (MQ=255)
cacacGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTcta > 1:892652/1‑71 (MQ=255)
acacGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctac > 1:845018/1‑71 (MQ=255)
cacGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAAtt > 1:2832409/1‑66 (MQ=255)
cacGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctac > 1:898924/1‑70 (MQ=255)
acGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctacta < 1:2682602/71‑1 (MQ=255)
cGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctact > 1:2200472/1‑69 (MQ=255)
gCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAg > 1:2578482/1‑71 (MQ=255)
gCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATAACTGGGTTCCAATTCTACTAAg > 1:2559504/1‑71 (MQ=255)
tgtgtgGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAAtt > 1:1768333/1‑61 (MQ=255)
tgtgGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCt < 1:2827380/71‑1 (MQ=255)
gtgGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCtt > 1:1899645/1‑71 (MQ=255)
ccTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGt < 1:2093923/69‑1 (MQ=255)
ccTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCa < 1:1160040/71‑1 (MQ=255)
cTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTc < 1:1952681/69‑1 (MQ=255)
cTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaa < 1:1148183/71‑1 (MQ=255)
tGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTcta > 1:2234960/1‑52 (MQ=255)
tGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaa > 1:1050963/1‑70 (MQ=255)
cGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaa < 1:935177/69‑1 (MQ=255)
aTAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGt < 1:1166394/63‑1 (MQ=255)
aTAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAAcc < 1:1218198/71‑1 (MQ=255)
aTAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAAcc < 1:284848/71‑1 (MQ=255)
tAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAAcc > 1:2183414/1‑70 (MQ=255)
tAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCt < 1:13189/71‑1 (MQ=255)
ttCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAAtt > 1:1725024/1‑38 (MQ=255)
ttCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAg < 1:1765722/40‑1 (MQ=255)
ttCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAg < 1:2437096/40‑1 (MQ=255)
ttCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGt < 1:3114135/50‑1 (MQ=255)
tCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaaaa > 1:2991529/1‑55 (MQ=255)
cGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAAc > 1:1949402/1‑61 (MQ=255)
cGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTtct < 1:297403/69‑1 (MQ=255)
cGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTtct < 1:2960151/69‑1 (MQ=255)
cGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTtct < 1:2818701/69‑1 (MQ=255)
cAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCtcatca < 1:878618/70‑1 (MQ=255)
cGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaaaa > 1:812984/1‑45 (MQ=255)
aTCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCtca > 1:172633/1‑58 (MQ=255)
tCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTc < 1:2274122/35‑1 (MQ=255)
tCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAAc > 1:2493527/1‑41 (MQ=255)
ttCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTa < 1:2157526/71‑1 (MQ=255)
|
CAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTA > W3110S.gb/2866043‑2866176
|
| 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
