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 I78 R1
|
12 |
11.6 |
697012 |
95.6% |
666343 |
85.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,877,246 |
A→T |
intergenic (‑157/‑140) |
dnaA ← / → BW25113_RS25780 |
chromosomal replication initiator protein DnaA/protein YsdD |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,877,246 | 0 | A | T | 100.0%
| 64.1
/ NA
| 18 | intergenic (‑157/‑140) | dnaA/BW25113_RS25780 | chromosomal replication initiator protein DnaA/protein YsdD |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base T (6/12); total (6/12) |
AAAAGACCCTGCTTGAGGGTGACGCACGAACCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTGCAAAACGATCGGGACCGCGGATCATAGCCTAAACTGCGCAAGAGATCTTCTGTTTCTCACAGATTTTCCCGATTTATCCACAGGACTTTCCAGAACTCGCTAAGT > NZ_CP009273/3877160‑3877330
|
aaaaGACCCTGCTTGAGGGTGACGCACGAACCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTGCAAAACGATCGGGACCGCGGTTCa < 2:334247/90‑1 (MQ=255)
aaaaGACCCTGCTTGAGGGTGACGCACGAACCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTGCAAAACGATCGGGACCGCGGTTCa < 2:302145/90‑1 (MQ=255)
aaaaGACCCTGCTTGAGGGTGACGCACGAACCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTGCAAAACGATCGGGACCGCGGTTCa < 2:228130/90‑1 (MQ=255)
aaGACCCTGCTTGAGGGTGACGCACGAACCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTGCAAAACGATCGGGACCGCGGTTCATa < 2:234265/90‑1 (MQ=255)
ccTGCTTGAGGGTGACGCACGAACCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTGCAAAACGATCGGGACCGCGGTTCA‑AGCCTaa > 2:87480/1‑90 (MQ=255)
gTGACGCACGAACCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTGCAAAACGATCGGGACCGCGGTTCATAGCCTAAACTGCGCAag < 2:294017/90‑1 (MQ=255)
gACGCACGAACCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTGCAAAACGATCGGGACCGCGGTTCa > 2:211973/1‑70 (MQ=255)
gACGCACGAACCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTGCAAAACGATCGGGACCGCGGTTCa < 1:211973/70‑1 (MQ=255)
gCACGAACCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTGCAAAACGATCGGGACCGCGGTTCATAGCCTAAACTGCGCAAGAGAtc > 1:244850/1‑90 (MQ=255)
atatGCCCGATCAAGATCCTGCAAAACGATCGGGACCGCGGTTCATAGCCTAAACTGCGCAAGAGATCTTCTGTTTCTCACAGATTTTcc < 1:5377/90‑1 (MQ=255)
atatGCCCGATCAAGATCCTGCAAAACGATCGGGACCGCGGTTCATAGCCTAAACTGCGCAAGAGATCTTCTGTTTCTCACAGATTTTcc < 1:330658/90‑1 (MQ=255)
atatGCCCGATCAACATCCTGCAAAACGATCGGGACCGCGGTTCATAGCCTAAACTGCGCAAGAGATCTTCTGTTTCTCACAGATTTTcc < 1:108665/90‑1 (MQ=255)
cGATCAAGATCCTGCAAAACGATCGGGACCGCGGTTCATAGCCTAAACTGCGCAAGAGATCTTCTGTTTCTCACAGATTTTCCCGATTTa < 1:339006/90‑1 (MQ=255)
aTCAAGATCCTGCAAAACGATCGGGACCGCGGTTCATAGCCTAAACTGCGCAAGAGATCTTCTGTTTCTCACAGATTTTCCCGATTTATc > 2:24933/1‑90 (MQ=255)
cTGCAAAACGATCGGGACCGCGGTTCATAGCCTAAACTGCGCAAGAGATCTTCTGTTTCTCACAGATTTTCCCGATTTATCCACAGGACt > 2:40193/1‑90 (MQ=255)
cTGCAAAACGATCGGGACCGCGGTTCATAGCCTAAACTGCGCAAGAGATCTTCTGTTTCTCACAGATTTTCCCGATTTATCCACAGGACt > 2:60750/1‑90 (MQ=255)
gACCGCGGTTCATAGCCTAAACTGCGCAAGAGATCTTCTGTTTCTCACAGATTTTCCCGATTTATCCACAGGACTTTCCAGAACTCGCTa < 2:40029/90‑1 (MQ=255)
cgcgGTTCATAGCCTAAACTGCGCAAGAGATCTTCTGTTTCTCACAGATTTTCCCGATTTATCCACAGGACTTTCCAGAACTCGCTAAgt < 2:108358/90‑1 (MQ=255)
|
AAAAGACCCTGCTTGAGGGTGACGCACGAACCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTGCAAAACGATCGGGACCGCGGATCATAGCCTAAACTGCGCAAGAGATCTTCTGTTTCTCACAGATTTTCCCGATTTATCCACAGGACTTTCCAGAACTCGCTAAGT > NZ_CP009273/3877160‑3877330
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
AAAAGACCCTGCTTGAGGGTGACGCACGAACCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTGCAAAACGATCGGGACCGCGGATCATAGCCTAAACTGCGCAAGAGATCTTCTGTTTCTCACAGATTTTCCCGATTTATCCACAGGACTTTCCAGAACTCGCTAAGTGTAAACGATCC > NZ_CP009273/3877160‑3877341
|
taagagacagGCTTGAGGGTGACGCACGAACCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTGCAAAACGATCGGGACCGCGGTTCATAGCCTAAAC < SRR3722216.214724/90‑1 (MQ=60)
TGAGGGTGACGCACGAACCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTGCAAAACGATCGGGACCGCGGTTCATAGCCTAAACTGCGCAAGAGATC > SRR3722216.248279/1‑100 (MQ=60)
ATATGCCCGATCAAGATCCTGCAAAACGATCGGGACCGCGGTTCATAGCCTAAACTGCGCAAGAGATCTTCTGTTTCTCACAGATTTTCCCGATTTATCC < SRR3722216.335532/100‑1 (MQ=60)
ATATGCCCGATCAAGATCCTGCAAAACGATCGGGACCGCGGTTCATAGCCTAAACTGCGCAAGAGATCTTCTGTTTCTCACAGATTTTCCCGATTTATCC < SRR3722216.5441/100‑1 (MQ=60)
ATATGCCCGATCAACATCCTGCAAAACGATCGGGACCGCGGTTCATAGCCTAAACTGCGCAAGAGATCTTCTGTTTCTCACAGATTTTCCCGATTTATCC < SRR3722216.109998/100‑1 (MQ=60)
CGATCAAGATCCTGCAAAACGATCGGGACCGCGGTTCATAGCCTAAACTGCGCAAGAGATCTTCTGTTTCTCACAGATTTTCCCGATTTATCCACAGGAC < SRR3722216.344020/100‑1 (MQ=60)
GATCAAGATCCTGCAAAACGATCGGGACCGCGGTTCATAGCCTAAACTGCGCctgtctcttatacacatctccgagcccacgagactaggcatgatctcg > SRR3722216.321793/1‑52 (MQ=60)
GCGGTTCATAGCCTAAACTGCGCAAGAGATCTTCTGTTTCTCACAGATTTTCCCGATTTATCCACAGGACTTTCCAGAACTCGCTAAGctgtctcttata > SRR3722216.110409/1‑88 (MQ=60)
|
AAAAGACCCTGCTTGAGGGTGACGCACGAACCGCTGTCTGCGGTTATATGCCCGATCAAGATCCTGCAAAACGATCGGGACCGCGGATCATAGCCTAAACTGCGCAAGAGATCTTCTGTTTCTCACAGATTTTCCCGATTTATCCACAGGACTTTCCAGAACTCGCTAAGTGTAAACGATCC > NZ_CP009273/3877160‑3877341
|
| 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: ‑ |
