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 |
|
A2 F17 I0 R1
|
71 |
95.7 |
2922988 |
91.7% |
2680379 |
65.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,620,867:1 |
+A |
100% |
coding (405/702 nt) |
eutQ ← |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,620,867 | 1 | . | A | 82.1%
| 104.5
/ 21.0
| 39 | coding (405/702 nt) | eutQ | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base . (7/0); new base A (0/32); total (7/32) |
| Fisher's exact test for biased strand distribution p-value = 6.50e-08 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
| Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch. |
TCAAGCCCACGCAATGCGGCTCTGCGCCGTCG‑AAACGACCAAACTTGACGCTACTGCCATCAATCACTTTGATGCCGCCTTTGCCGGTCACCGATTTGAAGC > minE/1620836‑1620937
|
tCAAGCCCACGCAATGCGGCTCTGCGCCGTCGAAAACGACCAAACTTGACGCTACTGCCATCAATCACttt < 1:514753/71‑1 (MQ=255)
tCAAGCCCACGCAATGCGGCTCTGCGCCGTCGAAAACGACCAAACTTGACGCTACTGCCATCAATCACttt < 1:368497/71‑1 (MQ=255)
tCAAGCCCACGCAATGCGGCTCTGCGCCGTCGAAAACGACCAAACTTGACGCTACTGCCATCAATCACttt < 1:313362/71‑1 (MQ=255)
tCAAGCCCACGCAATGCGGCTCTGCGCCGTCGAAAACGACCAAACTTGACGCTACTGCCATCAATCACttt < 1:263735/71‑1 (MQ=255)
tCAAGCCCACGCAATGCGGCTCTGCGCCGTCGAAAACGACCAAACTTGACGCTACTGCCATCAATCACttt < 1:25572/71‑1 (MQ=255)
tCAAGCCCACGCAATGCGGCTCTGCGCCGTCGAAAACGACCAAACTTGACGCTACTGCCATCAATCACttt < 1:410979/71‑1 (MQ=255)
tCAAGCCCACGCAATGCGGCTCTGCGCCGTCGAAAACGACCAAACTTGACGCTACTGCCATCAATCACttt < 1:2543949/71‑1 (MQ=255)
tCAAGCCCACGCAATGCGGCTCTGCGCCGTCGAAAACGACCAAACTTGACGCTACTGCCATCAATCACttt < 1:2531621/71‑1 (MQ=255)
tCAAGCCCACGCAATGCGGCTCTGCGCCGTCGAAAACGACCAAACTTGACGCTACTGCCATCAATCACttt < 1:2497528/71‑1 (MQ=255)
tCAAGCCCACGCAATGCGGCTCTGCGCCGTCGAAAACGACCAAACTTGACGCTACTGCCATCAATCACttt < 1:419844/71‑1 (MQ=255)
tCAAGCCCACGCAATGCGGCTCTGCGCCGTCGAAAACGACCAAACTTGACGCTACTGCCATCAATCACttt < 1:482003/71‑1 (MQ=255)
tCAAGCCCACGCAATGCGGCTCTGCGCCGTCGAAAACGACCAAACTTGACGCTACTGCCATCAATCACttt < 1:2302030/71‑1 (MQ=255)
tCAAGCCCACGCAATGCGGCTCTGCGCCGTCGAAAACGACCAAACTTGACGCTACTGCCATCAATCACttt < 1:1047637/71‑1 (MQ=255)
tCAAGCCCACGCAATGCGGCTCTGCGCCGTCGAAAACGACCAAACTTGACGCTACTGCCATCAATCACttt < 1:2182244/71‑1 (MQ=255)
tCAAGCCCACGCAATGCGGCTCTGCGCCGTCGAAAACGACCAAACTTGACGCTACTGCCATCAATCACttt < 1:2072396/71‑1 (MQ=255)
tCAAGCCCACGCAATGCGGCTCTGCGCCGTCGAAAACGACCAAACTTGACGCTACTGCCATCAATCACttt < 1:206432/71‑1 (MQ=255)
tCAAGCCCACGCAATGCGGCTCTGCGCCGTCGAAAACGACCAAACTTGACGCTACTGCCATCAATCACttt < 1:1904355/71‑1 (MQ=255)
tCAAGCCCACGCAATGCGGCTCTGCGCCGTCGAAAACGACCAAACTTGACGCTACTGCCATCAATCACttt < 1:1816445/71‑1 (MQ=255)
tCAAGCCCACGCAATGCGGCTCTGCGCCGTCGAAAACGACCAAACTTGACGCTACTGCCATCAATCACttt < 1:1811769/71‑1 (MQ=255)
tCAAGCCCACGCAATGCGGCTCTGCGCCGTCGAAAACGACCAAACTTGACGCTACTGCCATCAATCACttt < 1:585932/71‑1 (MQ=255)
tCAAGCCCACGCAATGCGGCTCTGCGCCGTCGAAAACGACCAAACTTGACGCTACTGCCATCAATCACttt < 1:1724784/71‑1 (MQ=255)
tCAAGCCCACGCAATGCGGCTCTGCGCCGTCGAAAACGACCAAACTTGACGCTACTGCCATCAATCACttt < 1:170338/71‑1 (MQ=255)
tCAAGCCCACGCAATGCGGCTCTGCGCCGTCGAAAACGACCAAACTTGACGCTACTGCCATCAATCACttt < 1:1699704/71‑1 (MQ=255)
tCAAGCCCACGCAATGCGGCTCTGCGCCGTCGAAAACGACCAAACTTGACGCTACTGCCATCAATCACttt < 1:1616930/71‑1 (MQ=255)
tCAAGCCCACGCAATGCGGCTCTGCGCCGTCGAAAACGACCAAACTTGACGCTACTGCCATCAATCACttt < 1:1535059/71‑1 (MQ=255)
tCAAGCCCACGCAATGCGGCTCTGCGCCGTCGAAAACGACCAAACTTGACGCTACTGCCATCAATCACttt < 1:1499691/71‑1 (MQ=255)
tCAAGCCCACGCAATGCGGCTCTGCGCCGTCGAAAACGACCAAACTTGACGCTACTGCCATCAATCACttt < 1:1485021/71‑1 (MQ=255)
tCAAGCCCACGCAATGCGGCTCTGCGCCGTCGAAAACGACCAAACTTGACGCTACTGCCATCAATCACttt < 1:640581/71‑1 (MQ=255)
tCAAGCCCACGCAATGCGGCTCTGCGCCGTCGAAAACGACCAAACTTGACGCTACTGCCATCAATCACttt < 1:1181742/71‑1 (MQ=255)
tCAAGCCCACGCAATGCGGCTCTGCGCCGTCGAAAACGACCAAACTTGACGCTACTGCCATCAATCACttt < 1:1109129/71‑1 (MQ=255)
tCAAGCCCACGCAATGCGGCTCTGCGCCGTCGAAAACGACCAAACTTGACGCTACTGCCATCAATCACttt < 1:867937/71‑1 (MQ=255)
cAAGCCCACGCAATGCGGCTCTGCGCCGTCGAAAACGACCAAACTTGACGCTACTGCCATCAATCACttt < 1:2189017/70‑1 (MQ=255)
cGGCTCTGCGCCGTCG‑AAACGACCAAACTTGACGCTACTGCCATCAATCACTTTGATGCCGCCTTTGCCgg > 1:2475677/1‑71 (MQ=255)
cGGCTCTGCGCCGTCG‑AAACGACCAAACTTGACGCTACTGCCATCAATCACTTTGATGCCGCCTTTGCCgg > 1:1278827/1‑71 (MQ=255)
cGGCTCTGCGCCGTCG‑AAACGACCAAACTTGACGCTACTGCCATCAATCACTTTGATGCCGCCTTTGCCgg > 1:1077688/1‑71 (MQ=255)
cGGCTCTGCGCCGTCG‑AAACGACCAAACTTGACGCTACTGCCATCAATCACTTTGATGCCGCCTTTGCCg > 1:82854/1‑70 (MQ=255)
tGCGCCGTCG‑AAACGACCAAACTTGACGCTACTGCCATCAATCACTTTGATGCCGCCTTTGCCGGTCAcc > 1:2453209/1‑70 (MQ=255)
tGCGCCGTCG‑AAACGACCAAACTTGACGCTACTGCCATCAATCACTTTGATGCCGCCTTTGCCGGTCAcc > 1:1754692/1‑70 (MQ=255)
tGCGCCGTCG‑AAACGACCAAACTTGACGCTACTGCCATCAATCACTTTGATGCCGCCTTTGCCGGTCAc > 1:2043608/1‑69 (MQ=255)
g‑AAACGACCAAACTTGACGCTACTGCCATCAATCACTTTGATGCCGCCTTTGCCGGTCACCGATTTGAAGc < 1:2553203/71‑1 (MQ=255)
|
TCAAGCCCACGCAATGCGGCTCTGCGCCGTCG‑AAACGACCAAACTTGACGCTACTGCCATCAATCACTTTGATGCCGCCTTTGCCGGTCACCGATTTGAAGC > minE/1620836‑1620937
|
| 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
