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 I209 R1
|
216 |
14.4 |
815930 |
96.1% |
784108 |
85.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
539,975 |
A→G |
D258D (GAT→GAC) |
allC ← |
allantoate deiminase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 539,975 | 0 | A | G | 92.3%
| 35.4
/ ‑5.7
| 13 | D258D (GAT→GAC) | allC | allantoate deiminase |
| Reads supporting (aligned to +/- strand): ref base A (0/0); major base G (7/5); minor base T (1/0); total (8/5) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GAACGTGGTTTTACCCGGCACCACATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGATCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAACCCATCGGCG > NZ_CP009273/539900‑540060
|
gAACGTGGTTTTACCCGGCACCACATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCtttt > 2:324804/1‑90 (MQ=255)
tATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGTTCGCCCATCCTTTTCGCTTTTTCGTCCCACTGATGGCAAATGCGAc > 1:275889/1‑90 (MQ=255)
tATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGAc > 1:272650/1‑90 (MQ=255)
aTTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACt > 1:134146/1‑90 (MQ=255)
cGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGaa < 1:324804/90‑1 (MQ=255)
tGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCac < 2:272650/90‑1 (MQ=255)
gCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGa > 1:296237/1‑71 (MQ=255)
gCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGa < 2:296237/71‑1 (MQ=255)
gCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCacg < 1:346880/90‑1 (MQ=255)
aGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGAt < 1:381600/90‑1 (MQ=255)
aGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAACCCATCGGc > 1:7485/1‑90 (MQ=255)
aGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAACCCATCGGc > 2:130565/1‑90 (MQ=255)
gCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAACCCATCGGCg > 1:137257/1‑90 (MQ=255)
|
GAACGTGGTTTTACCCGGCACCACATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGATCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAACCCATCGGCG > NZ_CP009273/539900‑540060
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ 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
ACATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGATCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAACCCATCGGCG > NZ_CP009273/539922‑540060
|
ACATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGTTCGCCCATCCTTTTCGCTTTTTCGTCCCACTGATGGCAAATGCGAC > SRR3722091.280442/1‑100 (MQ=60)
ACATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGAC > SRR3722091.277135/1‑100 (MQ=60)
CATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACT > SRR3722091.136160/1‑100 (MQ=60)
CGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACT < SRR3722091.330432/100‑1 (MQ=60)
GCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACctgtctctt > SRR3722091.301255/1‑91 (MQ=60)
GCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAACCC < SRR3722091.352956/100‑1 (MQ=60)
AGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAACCCATCGG < SRR3722091.388339/100‑1 (MQ=60)
GGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAACCCATCGGC > SRR3722091.7594/1‑100 (MQ=60)
GTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAACCCATCGGCG > SRR3722091.139314/1‑100 (MQ=60)
|
ACATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGATCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAACCCATCGGCG > NZ_CP009273/539922‑540060
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
