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 I229 R1
|
214 |
17.4 |
943020 |
97.5% |
919444 |
87.1 |
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%
| 82.8
/ NA
| 21 | coding (134/1878 nt) | bglF | PTS beta‑glucoside transporter subunit IIABC |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base . (12/9); total (12/9) |
CCAGGAAGACATCGGCCACATGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTCTTTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATG > NZ_CP009273/3898741‑3898907
|
ccAGGAAGACATCGGCCACATGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTCttttcag < 2:130724/90‑4 (MQ=255)
aGGAAGACATCGGCCCCATGGTTACCTATGACCACCTGAAGCTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTa > 2:463985/1‑90 (MQ=255)
aTCGGCCACATGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCt < 2:331843/90‑1 (MQ=255)
cGGCCACATGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTg < 1:244971/90‑1 (MQ=255)
cGGCCACATGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTg < 1:312645/90‑1 (MQ=255)
gACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCttt > 1:114325/1‑90 (MQ=255)
accTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACct > 2:361707/1‑60 (MQ=255)
accTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACct < 1:361707/60‑1 (MQ=255)
accTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCtttaatt > 2:125336/1‑90 (MQ=255)
cGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGt < 1:125336/90‑1 (MQ=255)
tCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTgcgc < 2:49584/90‑1 (MQ=255)
caccaccaTAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCaa < 2:370893/90‑1 (MQ=255)
accaccaTAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAAt < 2:251976/90‑1 (MQ=255)
ccaccaTAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATg > 2:395950/1‑90 (MQ=255)
ataataCCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGAc > 1:120055/1‑90 (MQ=255)
aCCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTcaca > 1:166799/1‑90 (MQ=255)
gggggTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTca < 2:8270/85‑1 (MQ=255)
gggggTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTca > 1:8270/1‑85 (MQ=255)
gggggTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATg > 2:453081/1‑90 (MQ=255)
gggggTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATg > 2:454962/1‑90 (MQ=255)
gggggTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATg > 2:190134/1‑90 (MQ=255)
gggggTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATg > 1:169136/1‑90 (MQ=255)
|
CCAGGAAGACATCGGCCACATGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTCTTTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATG > NZ_CP009273/3898741‑3898907
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 33 ≤ 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
AAGACATCGGCCACATGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTCTTTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATGTTATCTGCGCCCCCGACT > NZ_CP009273/3898746‑3898925
|
gagatgtgtataagagacagACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCCGTACCTCTGCTTGCGC < SRR3722113.365413/80‑1 (MQ=60)
CGGCCACATGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTT < SRR3722113.247092/100‑1 (MQ=60)
CGGCCACATGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTT < SRR3722113.315679/100‑1 (MQ=60)
GGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTT > SRR3722113.115320/1‑100 (MQ=60)
CGCTTTCCACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGC < SRR3722113.126402/100‑1 (MQ=60)
CACCACCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGAC > SRR3722113.121090/1‑100 (MQ=60)
CCATAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACA > SRR3722113.168152/1‑100 (MQ=60)
TAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATG > SRR3722113.170502/1‑100 (MQ=60)
TAATAATACCGGGGGTC‑TTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATG > SRR3722113.8349/1‑100 (MQ=60)
TTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATGTTATCctgtctcttatac > SRR3722113.316247/1‑87 (MQ=60)
TTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATGTTATCTGCGCCCCCGACT > SRR3722113.134472/1‑100 (MQ=60)
TTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATGTTATCTGCGCCCCCGACT > SRR3722113.431550/1‑100 (MQ=60)
|
AAGACATCGGCCACATGGTTACCTATGACCACCTGAAACTGGCCACCGCTTTCCACCACCATAATAATACCGGGGGTCTTTTTCAGTACCTCTGCTTGCGCTTTGCTTTCATCCTTTAATTTAAAACGTAATCGCGTTGCGCAATGCATCAGACTCACAATGTTATCTGCGCCCCCGACT > NZ_CP009273/3898746‑3898925
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
