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 F2 I231 R1
|
218 |
12.8 |
703680 |
97.2% |
683976 |
86.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,898,828 |
(T)5→4 |
coding (130/1878 nt) |
bglF ← |
PTS beta‑glucoside transporter subunit IIABC |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,898,824 | 0 | T | . | 100.0%
| 46.7
/ NA
| 12 | coding (134/1878 nt) | bglF | PTS beta‑glucoside transporter subunit IIABC |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base . (6/6); total (6/6) |
ACCGCCAGGAAGACATCGGCCACATGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTCTTTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATG > NZ_CP009273/3898737‑3898907
|
aCCGCCAGGAAGACATCGGCCACATGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTCttt < 1:218530/90‑1 (MQ=255)
ccAGGAAGACATCGGCCACATGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTCttttcag > 1:108095/1‑87 (MQ=255)
caTGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCgcttt < 2:165240/90‑1 (MQ=255)
ccTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCAt < 2:5153/90‑1 (MQ=255)
accTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCtttaatt > 1:320992/1‑90 (MQ=255)
gCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAAt > 1:98721/1‑90 (MQ=255)
tCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTgcgc < 1:327280/90‑1 (MQ=255)
ataCCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTca < 2:308092/90‑1 (MQ=255)
aCCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTcaca < 1:63378/90‑1 (MQ=255)
gggggTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTca > 1:335286/1‑85 (MQ=255)
gggggTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTca < 2:335286/85‑1 (MQ=255)
gggggTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATg > 1:56815/1‑90 (MQ=255)
gggggTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATg > 2:90593/1‑90 (MQ=255)
gggggTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATg > 2:90866/1‑90 (MQ=255)
|
ACCGCCAGGAAGACATCGGCCACATGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTCTTTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATG > NZ_CP009273/3898737‑3898907
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CTGTTAACCGCCAGGAAGACATCGGCCACATGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTCTTTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATGTTATCTG > NZ_CP009273/3898731‑3898914
|
CTGTTAACCGCCAGGAAGACATCGGCCACATGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAG > SRR3722116.109412/1‑100 (MQ=60)
gcagcgtcagatgtgtataagagacagTGGTTACCTATGACCACCTTAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTAC < SRR3722116.310534/73‑1 (MQ=60)
ACCGCCAGGAAGACATCGGCCACATGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTC < SRR3722116.221398/100‑1 (MQ=60)
ACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATT > SRR3722116.325766/1‑100 (MQ=60)
CCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAAT > SRR3722116.99932/1‑100 (MQ=60)
TCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAG < SRR3722116.332150/100‑1 (MQ=60)
TAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATG > SRR3722116.340287/1‑100 (MQ=60)
TAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATG > SRR3722116.57515/1‑100 (MQ=60)
ATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATGTTATC > SRR3722116.275849/1‑100 (MQ=60)
ACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATGTTATCTG < SRR3722116.64162/100‑1 (MQ=60)
|
CTGTTAACCGCCAGGAAGACATCGGCCACATGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTCTTTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATGTTATCTG > NZ_CP009273/3898731‑3898914
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
