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 |
|
A1 F8 I0 R1
|
311 |
50.1 |
4085234 |
95.9% |
3917739 |
60.7 |
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%
| 140.5
/ NA
| 47 | 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 (20/27); total (20/27) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
CAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCAT > W3110S.gb/2866043‑2866173
|
cAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAAt > 1:61263/1‑70 (MQ=255)
aaCACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTc < 1:130825/71‑1 (MQ=255)
cacGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctact < 1:1359544/71‑1 (MQ=255)
actcTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctact < 1:3572888/67‑1 (MQ=255)
tgtgtgGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTc < 1:3267811/62‑1 (MQ=255)
tgtgtgGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTc < 1:1221559/62‑1 (MQ=255)
tgtgtgGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTc < 1:1264929/62‑1 (MQ=255)
gCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCtttt < 1:266578/70‑1 (MQ=255)
gCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTc > 1:2342499/1‑71 (MQ=255)
tCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctac < 1:1477091/57‑1 (MQ=255)
tCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctac < 1:1803303/57‑1 (MQ=255)
gCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaa > 1:3148226/1‑70 (MQ=255)
gCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaa > 1:1176496/1‑69 (MQ=255)
cGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaaa < 1:2443669/70‑1 (MQ=255)
cGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaaa < 1:109418/70‑1 (MQ=255)
cGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaa < 1:280435/69‑1 (MQ=255)
cGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaa < 1:825490/69‑1 (MQ=255)
gATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTc < 1:2810168/47‑1 (MQ=255)
gATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTc < 1:2965132/47‑1 (MQ=255)
tAACAGTTCCTCTTCGGCCAAATCGTAATCACTGGCTTCCAAATcta > 1:1894519/1‑47 (MQ=255)
aaCAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTc > 1:2534169/1‑59 (MQ=255)
aCAGTTCCTCTTCGGCCAATTCGTTATCACTGGGTTCCAAtt > 1:38054/1‑42 (MQ=38)
aCAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTc < 1:3160280/70‑1 (MQ=255)
aCAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTc < 1:384714/70‑1 (MQ=255)
ttCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTc < 1:1457695/39‑1 (MQ=255)
ccTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCg > 1:1111416/1‑71 (MQ=255)
ccTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCg > 1:1917197/1‑71 (MQ=255)
ttCGGCCAAATCGTTATCACTGGGTTCCAATTctac > 1:2391848/1‑36 (MQ=255)
ttCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTtct > 1:3291223/1‑71 (MQ=255)
cGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCtca > 1:2996192/1‑71 (MQ=255)
cGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCtca > 1:148950/1‑71 (MQ=255)
aaTCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTc < 1:2810856/52‑1 (MQ=255)
aTCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaaa < 1:3982142/46‑1 (MQ=255)
tCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTc < 1:3803761/71‑1 (MQ=255)
cGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCa > 1:477697/1‑41 (MQ=255)
cGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTcc > 1:2961383/1‑71 (MQ=255)
gTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGt > 1:3391402/1‑56 (MQ=255)
gTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCg < 1:1350758/71‑1 (MQ=255)
gTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCg < 1:28692/71‑1 (MQ=255)
tATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCa > 1:3922761/1‑71 (MQ=255)
aTCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCAt > 1:2255791/1‑71 (MQ=255)
aTCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCAt > 1:3097765/1‑71 (MQ=255)
tCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATc < 1:952989/71‑1 (MQ=255)
tcTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaa < 1:3603482/35‑1 (MQ=255)
tGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTc < 1:481637/40‑1 (MQ=255)
gggTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCAt > 1:240600/1‑71 (MQ=255)
ttCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCg < 1:1917079/59‑1 (MQ=255)
|
CAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCAT > W3110S.gb/2866043‑2866173
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
