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 F1 I0 R1
|
92 |
46.1 |
3712835 |
96.9% |
3597737 |
60.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,824,410 |
T→A |
100% |
pseudogene (543/687 nt) |
rph → |
ECK3633:JW3618:b3643; ribonuclease PH |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,824,410 | 0 | T | A | 99.0%
| 161.9
/ ‑6.2
| 58 | pseudogene (543/687 nt) | rph | ECK3633:JW3618:b3643; ribonuclease PH |
| Reads supporting (aligned to +/- strand): ref base T (0/0); major base A (23/34); minor base C (1/0); total (24/34) |
| Fisher's exact test for biased strand distribution p-value = 4.14e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
AGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGCAGGGGACGG > W3110S.gb/3824344‑3824477
|
aGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCg > 1:3464116/1‑71 (MQ=255)
cGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCg > 1:803879/1‑68 (MQ=255)
tttCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCag < 1:877753/66‑1 (MQ=255)
tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa > 1:515962/1‑71 (MQ=255)
tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa > 1:2270233/1‑71 (MQ=255)
tGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACa > 1:418140/1‑71 (MQ=255)
tGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACa > 1:3711375/1‑71 (MQ=255)
gTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa < 1:2964650/60‑1 (MQ=255)
tCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATg < 1:3533300/71‑1 (MQ=255)
aTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAAc > 1:1109122/1‑69 (MQ=255)
aTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAAc > 1:910156/1‑69 (MQ=255)
aTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAAc > 1:662375/1‑69 (MQ=255)
aTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg < 1:1591543/70‑1 (MQ=255)
ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCg < 1:3385335/51‑1 (MQ=255)
ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCg < 1:1670337/51‑1 (MQ=255)
ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa < 1:1188343/53‑1 (MQ=255)
ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGt < 1:458719/70‑1 (MQ=255)
taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCaga > 1:2828120/3‑52 (MQ=255)
taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtg < 1:664290/69‑1 (MQ=255)
taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt < 1:2129204/68‑1 (MQ=255)
cGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgatga > 1:3638070/1‑71 (MQ=255)
gtgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAgaga < 1:650955/46‑1 (MQ=37)
tgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCagag < 1:2925823/45‑1 (MQ=37)
tgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCg < 1:1299847/70‑1 (MQ=255)
tttGCGATCTGGAATACGTTGAAGACTCAGCCGCa < 1:352571/35‑1 (MQ=255)
tttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGaa > 1:400117/1‑65 (MQ=255)
tGCGATCTGGAATACGTTGAAGACTCAGCCGCagag > 1:3422984/1‑36 (MQ=255)
tGCGATCTGGAATACGTTGAAGACTCAGCCGCaga > 1:1809626/1‑35 (MQ=255)
tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAAc > 1:1157516/1‑48 (MQ=255)
tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCg > 1:1495965/1‑61 (MQ=255)
gCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCg > 1:1354338/1‑39 (MQ=255)
gCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGaa < 1:2321117/62‑1 (MQ=255)
tCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAg < 1:1793489/59‑1 (MQ=255)
tCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAg < 1:1703470/59‑1 (MQ=255)
cTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGAAGGGCGcatcat > 1:1600898/1‑71 (MQ=255)
tGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAAc > 1:1849178/1‑41 (MQ=255)
tGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgatg < 1:2752136/50‑1 (MQ=255)
tGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGgcg < 1:1339352/64‑1 (MQ=255)
gAATACGTTGAAGACTCAGCCGCATAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGcat < 1:2234586/65‑1 (MQ=255)
gAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGcatca < 1:1724535/67‑1 (MQ=255)
gAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTg < 1:2928523/70‑1 (MQ=255)
gAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTg > 1:2170458/1‑70 (MQ=255)
gAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGa < 1:695577/71‑1 (MQ=255)
gAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGa < 1:119976/71‑1 (MQ=255)
gAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGa < 1:1058957/71‑1 (MQ=255)
tACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGgcgc < 1:3129611/60‑1 (MQ=255)
tACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTg < 1:1886258/67‑1 (MQ=255)
tACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGa < 1:1475002/68‑1 (MQ=255)
cGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGc < 1:2455833/71‑1 (MQ=255)
gTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTg < 1:20404/64‑1 (MQ=255)
gTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGc < 1:3469725/70‑1 (MQ=255)
ttGAAGACTCAGCTGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGc < 1:1326882/69‑1 (MQ=255)
ttGAAGACTCAGCCGCAGAGACCGACATGAAGGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGCAg > 1:425763/1‑71 (MQ=255)
tGAAGACTCCGCCGCAGAGACCGCCATGAACGTAGTGATGAc > 1:1393288/1‑42 (MQ=38)
gAAGACTCAGCCGCAGAGACCGACATGAACGTAGt > 1:469570/1‑35 (MQ=255)
gAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGaa > 1:3678116/1‑63 (MQ=255)
aaGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGCAggg < 1:2425299/70‑1 (MQ=255)
gACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGCAggg < 1:1438715/68‑1 (MQ=255)
ctcaGCCGCAGAGACCGACATGAACGTAGTGATGACCGaa < 1:2284837/40‑1 (MQ=255)
ctcaGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGCAGGGGACgg > 1:1635975/1‑71 (MQ=255)
|
AGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGCAGGGGACGG > W3110S.gb/3824344‑3824477
|
| 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
