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 |
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%
| 167.3
/ NA
| 48 | pseudogene (666/687 nt) | rph | ECK3633:JW3618:b3643; ribonuclease PH |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base G (17/31); total (17/31) |
| 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. |
AAGGCGAGCCGTTCACCCATGAAGAGCTACTCATCTTGTTGGCTCTGGCCCGA‑GGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGC > W3110S.gb/3824481‑3824593
|
aaGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCa < 1:1198614/69‑1 (MQ=255)
aaGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCa < 1:3304901/69‑1 (MQ=255)
ttCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCAt < 1:550770/59‑1 (MQ=255)
ttCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCAt < 1:2149201/59‑1 (MQ=255)
ttCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCAt < 1:358155/59‑1 (MQ=255)
ttCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCAt < 1:3465505/59‑1 (MQ=255)
ttCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCAt < 1:172658/59‑1 (MQ=255)
tCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCAt < 1:1885036/58‑1 (MQ=255)
aCCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGaa < 1:1476005/71‑1 (MQ=255)
aCCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGaa < 1:2376607/71‑1 (MQ=255)
aCCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGaa < 1:2911268/71‑1 (MQ=255)
aCCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGaa < 1:2960663/71‑1 (MQ=255)
aCCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGaa < 1:1994305/71‑1 (MQ=255)
aCCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGaa < 1:1491893/71‑1 (MQ=255)
aCCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGaa < 1:698876/71‑1 (MQ=255)
gAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcgaat > 1:2499300/1‑46 (MQ=255)
gAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcgaat > 1:3618079/1‑46 (MQ=255)
aaGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGAGACGCAGAAggcgg > 1:1361894/1‑69 (MQ=255)
aaGAGCTACTCACCTTCTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGgcggcg > 1:2307142/1‑71 (MQ=255)
agagCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCAATTGTAGCGACGCAGAAGGCGgcgc > 1:1163830/1‑71 (MQ=255)
ggtACTCACCTTGTTGGCGCTGGCCCGAGGGGGAAGCGAATCCAt < 1:371261/43‑1 (MQ=255)
cTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATcc < 1:2855204/39‑1 (MQ=25)
cTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATcc < 1:2971979/39‑1 (MQ=25)
cTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATcc < 1:2565044/39‑1 (MQ=25)
cTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATcc < 1:1040105/39‑1 (MQ=25)
cTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCTCTGGCa < 1:2426/69‑1 (MQ=255)
cTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCa < 1:838604/69‑1 (MQ=255)
cTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCa < 1:2574147/69‑1 (MQ=255)
caccTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACt > 1:1004959/4‑71 (MQ=255)
caccTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACt > 1:2217041/4‑71 (MQ=255)
caccTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACt > 1:1675958/4‑71 (MQ=255)
caccTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACt > 1:1181836/4‑71 (MQ=255)
caccTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACt > 1:1184974/4‑71 (MQ=255)
caccTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACt > 1:3162853/4‑71 (MQ=255)
caccTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACt > 1:1571660/4‑71 (MQ=255)
caccTTGTTGGCGCTGGCCCGAGGGGGAATCCAATCCATAGTAGCGACGCAGAAGGCGGCGCTGGCAAACt > 1:1231838/4‑71 (MQ=255)
accTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAAc < 1:3613840/67‑1 (MQ=255)
tgttgGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCATAAGGCGGCGCTGGCAAACTGAtt > 1:1110057/1‑70 (MQ=255)
tgttgGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAtt > 1:3456371/1‑70 (MQ=255)
tgttgGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAtt > 1:2988205/1‑70 (MQ=255)
tgttgGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAtt > 1:246626/1‑70 (MQ=255)
gctGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGc < 1:1326081/70‑1 (MQ=255)
gctGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGc < 1:253504/70‑1 (MQ=255)
gctGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGc < 1:3346461/70‑1 (MQ=255)
gctGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGc < 1:3156188/70‑1 (MQ=255)
gctGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGc < 1:1060000/70‑1 (MQ=255)
gctGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGc < 1:745292/70‑1 (MQ=255)
ctGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGc < 1:2344530/70‑1 (MQ=255)
|
AAGGCGAGCCGTTCACCCATGAAGAGCTACTCATCTTGTTGGCTCTGGCCCGA‑GGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGC > W3110S.gb/3824481‑3824593
|
| 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
