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 |
3,824,533:1 |
+G |
100% |
pseudogene (666/687 nt) |
rph → |
ECK3633:JW3618:b3643; ribonuclease PH |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,824,533 | 1 | . | G | 100.0%
| 151.1
/ NA
| 44 | pseudogene (666/687 nt) | rph | ECK3633:JW3618:b3643; ribonuclease PH |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base G (18/26); total (18/26) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
| Rejected as polymorphism: Polymorphic base substitution creates a homopolymer stretch. |
AAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCATCTTGTTGGCTCTGGCCCGA‑GGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGCGACTG > W3110S.gb/3824463‑3824598
|
aaGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGa < 1:1389113/71‑1 (MQ=255)
aaGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGa < 1:2051571/71‑1 (MQ=255)
tGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑ggg < 1:2167565/71‑1 (MQ=255)
gACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcg < 1:134100/71‑1 (MQ=255)
gACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcg < 1:39338/71‑1 (MQ=255)
gACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑g > 1:618025/1‑62 (MQ=255)
ggCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcgaat > 1:3408866/1‑71 (MQ=255)
ggCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcgaat > 1:3998854/1‑71 (MQ=255)
aGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCa < 1:1141341/71‑1 (MQ=255)
aGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCa < 1:3230585/71‑1 (MQ=255)
gAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCAt < 1:3462963/71‑1 (MQ=255)
aaGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCAtt < 1:2700183/71‑1 (MQ=255)
aaGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCAtt < 1:3793536/71‑1 (MQ=255)
ggCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGa > 1:1662046/1‑51 (MQ=255)
ggCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTg > 1:570979/1‑70 (MQ=255)
ggCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑g > 1:3108116/1‑52 (MQ=255)
gCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑gggg > 1:4091748/1‑54 (MQ=255)
gCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGa > 1:2282100/1‑71 (MQ=255)
gCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑gg > 1:3617612/1‑48 (MQ=255)
gTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACg > 1:3733219/1‑70 (MQ=255)
gTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑gg < 1:991475/45‑1 (MQ=255)
ttCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCa < 1:3111297/71‑1 (MQ=255)
cACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcgaat > 1:4007397/1‑53 (MQ=255)
aCCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGaa < 1:1756331/71‑1 (MQ=255)
cccATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcgaa > 1:3248831/1‑50 (MQ=255)
cccATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAg < 1:2741873/71‑1 (MQ=255)
ccATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAgg < 1:1178672/71‑1 (MQ=255)
ccATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAgg > 1:1509433/1‑71 (MQ=255)
ccATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAg > 1:2930205/1‑70 (MQ=255)
cATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGa > 1:2865023/1‑36 (MQ=37)
cATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGa > 1:2860100/1‑36 (MQ=37)
cATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAggc < 1:1239772/71‑1 (MQ=255)
aaGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAggcggc < 1:4206042/70‑1 (MQ=255)
aaGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAggcggc > 1:2996479/1‑70 (MQ=255)
aaGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAggcggc < 1:1850615/70‑1 (MQ=255)
aaGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGgcggcg > 1:1226727/1‑71 (MQ=255)
agagCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGgcgc > 1:3074312/1‑71 (MQ=255)
cTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCaaa > 1:2723110/1‑71 (MQ=255)
cTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGAGCTGGCa < 1:2648643/69‑1 (MQ=255)
tCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAAc > 1:2805043/1‑71 (MQ=255)
accTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACt < 1:2230721/68‑1 (MQ=255)
ccTTGTTGGCGCTGGCCCGAGGGGGAATCTAATcc < 1:2957367/34‑1 (MQ=16)
ccTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGa < 1:2152033/70‑1 (MQ=255)
cTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGa < 1:4147555/70‑1 (MQ=255)
ttgttgGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGGGCTGGCa < 1:684046/63‑1 (MQ=255)
gttgGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAtt > 1:1364537/1‑69 (MQ=255)
ttgGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGc < 1:1642077/43‑1 (MQ=37)
ttgGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAttttt < 1:4164157/71‑1 (MQ=255)
ttgGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAtttt > 1:2499112/1‑70 (MQ=255)
ggCGCTGGCCCGAGGGGGAATCGAATCCATTGTAg > 1:1719133/1‑35 (MQ=255)
ggCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTa < 1:3943329/70‑1 (MQ=255)
ctGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGCg < 1:3597966/71‑1 (MQ=255)
gCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAgg > 1:2975215/1‑40 (MQ=38)
gCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGCGACt < 1:2945730/71‑1 (MQ=255)
cccGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGCGACtg < 1:2164951/71‑1 (MQ=255)
|
AAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCATCTTGTTGGCTCTGGCCCGA‑GGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGCGACTG > W3110S.gb/3824463‑3824598
|
| 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
