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 R2
|
422 |
46.8 |
3726540 |
94.7% |
3529033 |
61.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
2,315,568 |
A→G |
100% |
G172G (GGT→GGC) |
ompC ← |
outer membrane porin protein C |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,315,568 | 0 | A | G | 96.1%
| 170.4
/ ‑1.7
| 51 | G172G (GGT→GGC) | ompC | outer membrane porin protein C |
| Reads supporting (aligned to +/- strand): ref base A (2/0); new base G (17/32); total (19/32) |
| Fisher's exact test for biased strand distribution p-value = 1.34e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.86e-01 |
| 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. |
CAGTGCGTCACGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGG > W3110S.gb/2315502‑2315628
|
cAGTGCGTCACGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGCCCt < 1:477697/71‑1 (MQ=255)
aCGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTGGTACTGaa > 1:2550401/1‑71 (MQ=255)
aCGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTGGTACTGaa > 1:3173759/1‑71 (MQ=255)
aCGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTGGTACTGaa > 1:1301929/1‑71 (MQ=255)
gttagttaCGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGt > 1:2656256/1‑71 (MQ=255)
gttagttaCGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGt > 1:2899758/1‑71 (MQ=255)
gttagttaCGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGt > 1:1823025/1‑71 (MQ=255)
tagttaCGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTGGt < 1:783179/54‑1 (MQ=255)
ttaCGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCa < 1:3683162/62‑1 (MQ=255)
ttaCGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCa < 1:3159059/62‑1 (MQ=255)
ccACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTc < 1:526571/71‑1 (MQ=255)
caaGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTgg < 1:1113679/40‑1 (MQ=38)
cTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTgg < 1:3194719/42‑1 (MQ=255)
aGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGccc > 1:2225821/1‑37 (MQ=255)
aGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGccc > 1:702326/1‑37 (MQ=255)
aGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGcc > 1:3358336/1‑36 (MQ=255)
aGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTGGTa > 1:1256370/1‑42 (MQ=255)
aGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTGGTa > 1:2925716/1‑42 (MQ=255)
aGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTGGTa > 1:2351787/1‑42 (MQ=255)
aGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTAc > 1:1721968/1‑43 (MQ=255)
aGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTAc > 1:1802518/1‑43 (MQ=255)
gTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGcc > 1:3484160/1‑35 (MQ=255)
aaaGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGa > 1:2287293/1‑70 (MQ=255)
aaGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAg < 1:3201735/68‑1 (MQ=255)
aaGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAg < 1:1101618/68‑1 (MQ=255)
aaGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAg < 1:250185/68‑1 (MQ=255)
ccTTCACCAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCg > 1:2536973/1‑69 (MQ=255)
ccTTCACCAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCg > 1:2697905/1‑69 (MQ=255)
ttCACCAGATGGGTTGCCGTTTTTGCCCTGGTACTGaa < 1:2274918/38‑1 (MQ=255)
ttCACCAGATGGGTTGCCGTTTTTGCCCTGGTACTGaa < 1:2173009/38‑1 (MQ=255)
ttCACCAGATGGGTTGCCGTTTTTGCCCTGGTACTGaa < 1:105748/38‑1 (MQ=255)
ttCACCAGATGGGTTGCCGTTTTTGCCCTGGTACTGaa < 1:553923/38‑1 (MQ=255)
ttCACCAGATGCGTTGCCGTTTTTGCCCTGGTACTGaa < 1:3506831/38‑1 (MQ=38)
tCACCAGATGGGTTGCCGTTTTTGCCCTGGTACTGaa < 1:2401936/37‑1 (MQ=255)
ccAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTc < 1:983070/71‑1 (MQ=255)
ccAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTc < 1:954718/71‑1 (MQ=255)
ccAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTc < 1:1143267/71‑1 (MQ=255)
ccAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTc < 1:654684/71‑1 (MQ=255)
ccAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTc < 1:128758/71‑1 (MQ=255)
ccAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTc < 1:3697049/71‑1 (MQ=255)
ccAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTc < 1:1626285/71‑1 (MQ=255)
ccAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTc < 1:2955392/71‑1 (MQ=255)
ccAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTc < 1:2603994/71‑1 (MQ=255)
ccAGATGCGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTc < 1:3630608/71‑1 (MQ=255)
tGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAgtgt < 1:1398619/71‑1 (MQ=255)
tGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAgtgt < 1:3628032/71‑1 (MQ=255)
tGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAgtgt < 1:1329529/71‑1 (MQ=255)
ggTTGCCGTTTTTGCCCTGGAACTGAACACCAAAGTTCAGCCCGTCAACCAGACCGAAGAAGTCAgtgt > 1:1820621/1‑69 (MQ=38)
gCCGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACgg < 1:1464128/70‑1 (MQ=255)
gCCGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACgg < 1:1497965/70‑1 (MQ=255)
ccGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTc < 1:2046411/59‑1 (MQ=255)
|
CAGTGCGTCACGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGG > W3110S.gb/2315502‑2315628
|
| 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
