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 |
2,061,342 |
T→A |
intergenic (‑576/‑774) |
BW25113_RS10415 ← / → BW25113_RS24005 |
IS5‑like element IS5 family transposase/TonB‑dependent receptor plug domain‑containing protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,061,342 | 0 | T | A | 100.0%
| 42.5
/ NA
| 12 | intergenic (‑576/‑774) | BW25113_RS10415/BW25113_RS24005 | IS5‑like element IS5 family transposase/TonB‑dependent receptor plug domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base A (6/6); total (6/6) |
CTTTTCTCAAATTCTGCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGATCATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGAAGCTA > NZ_CP009273/2061267‑2061417
|
cTTTTCTCAAATTCTGCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTg < 1:164342/90‑1 (MQ=255)
tctcAAATTCTGCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAGTACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGaa < 2:121526/90‑1 (MQ=255)
gCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAAcc > 1:326294/1‑90 (MQ=255)
cAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGa < 2:347778/90‑1 (MQ=255)
gACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGt < 1:145934/90‑1 (MQ=255)
gACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGt < 1:314666/90‑1 (MQ=255)
caGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCa > 2:346072/1‑90 (MQ=255)
ccATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGc > 1:342119/1‑69 (MQ=255)
ccATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGc < 2:342119/69‑1 (MQ=255)
aaaTACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATg > 2:153051/1‑90 (MQ=255)
gAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGAAGCTa > 1:253392/1‑90 (MQ=255)
gAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGAAGCTa > 2:243451/1‑90 (MQ=255)
|
CTTTTCTCAAATTCTGCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGATCATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGAAGCTA > NZ_CP009273/2061267‑2061417
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CTTTTCTCAAATTCTGCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGATCATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGAAGCTATTGTTGTGTTTTGTACATCAG > NZ_CP009273/2061267‑2061438
|
CTTTTCTCAAATTCTGCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAA < SRR3722116.166230/100‑1 (MQ=60)
CTCAAATTCTGCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACC > SRR3722116.331149/1‑100 (MQ=60)
GCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGctgtctcttatacacatctgacgctgccga > SRR3722116.155735/1‑70 (MQ=60)
GACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTC < SRR3722116.147621/100‑1 (MQ=60)
GACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTC < SRR3722116.319326/100‑1 (MQ=60)
GCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACctgtctcttat > SRR3722116.347212/1‑89 (MQ=60)
GCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGActgtctcttatacacatctgacgctgccgacgaagttggctgtgtagatctcggtggt > SRR3722116.2455/1‑42 (MQ=60)
GCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGAAGCTA > SRR3722116.256983/1‑100 (MQ=60)
GGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTctgtctcttatacacatctgacgctgccgacgaagttg > SRR3722116.59212/1‑62 (MQ=60)
|
CTTTTCTCAAATTCTGCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGATCATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGAAGCTATTGTTGTGTTTTGTACATCAG > NZ_CP009273/2061267‑2061438
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
