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 I195 R1
|
222 |
27.1 |
1551108 |
96.0% |
1489063 |
86.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
951,809 |
T→G |
T94P (ACC→CCC) |
ycaO ← |
30S ribosomal protein S12 methylthiotransferase accessory factor YcaO |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 951,809 | 0 | T | G | 100.0%
| 65.5
/ NA
| 20 | T94P (ACC→CCC) | ycaO | 30S ribosomal protein S12 methylthiotransferase accessory factor YcaO |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (12/8); total (12/8) |
AGCCCTTCTGGCACATCGTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGTTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCGAGTGCAGAAGCCAGCGCCG > NZ_CP009273/951727‑951889
|
agcCCTTCTGGCACATCGTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGccc > 2:79122/1‑90 (MQ=255)
agcCCTTCTGGCACATCGTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGccc > 1:88274/1‑90 (MQ=255)
cccTTCTGGCACATCGTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCccag > 1:299408/1‑90 (MQ=255)
cacaTCGTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTc > 2:41859/1‑90 (MQ=255)
cATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCaaaaa < 1:41859/90‑1 (MQ=255)
cATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCaaaaa > 2:763641/1‑90 (MQ=255)
tttCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCaaaaa < 1:178423/87‑1 (MQ=255)
tttCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCaaaaa > 2:178423/1‑87 (MQ=255)
ggTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAgtt < 1:710635/90‑1 (MQ=255)
ggTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAgtt < 1:739468/90‑1 (MQ=255)
cAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAgttggt > 2:541188/1‑90 (MQ=255)
gTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAgttggttg > 2:180777/1‑90 (MQ=255)
aaCCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTgagaga < 1:180777/90‑1 (MQ=255)
ttCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGaa < 2:709810/90‑1 (MQ=255)
gAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCGAGTGCAGa > 1:574995/1‑90 (MQ=255)
ggACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCGAGTGCAGAAGcc > 2:154812/1‑90 (MQ=255)
gACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCGAGTGCAGAAGCCa > 1:689143/1‑90 (MQ=255)
tGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCg > 2:528717/1‑59 (MQ=255)
tGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCg < 1:528717/59‑1 (MQ=255)
tGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCGAGTGCAGAAGCCAGcgccg < 2:574995/90‑1 (MQ=255)
|
AGCCCTTCTGGCACATCGTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGTTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCGAGTGCAGAAGCCAGCGCCG > NZ_CP009273/951727‑951889
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ 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
GTCATCGAGCAGCCCTTCTGGCACATCGTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGTTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCGAGTGCAGAAGCCAGCGCCGCTTTCTTGGTTGCGCCT > NZ_CP009273/951717‑951906
|
GTCATCGAGCAGCCCTTCTGGCACATCGTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCC > SRR3722073.90253/1‑100 (MQ=60)
CATCGAGCAGCCCTTCTGGCACATCGTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAG > SRR3722073.305741/1‑100 (MQ=60)
CATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGT < SRR3722073.181880/100‑1 (MQ=60)
CATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGT < SRR3722073.42874/100‑1 (MQ=60)
GGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGA < SRR3722073.724997/100‑1 (MQ=60)
GGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGA < SRR3722073.754441/100‑1 (MQ=60)
AACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAAT < SRR3722073.184270/100‑1 (MQ=60)
tcagatgtgtataagagacaGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCAC < SRR3722073.539786/80‑1 (MQ=60)
GATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCGAGTGCAGA > SRR3722073.587000/1‑100 (MQ=60)
TGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCGAGTGCAGAAGCCA > SRR3722073.703183/1‑100 (MQ=60)
GGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACtgtctcttatacacatctgacgctgccgacgatatgcagtgtgtagatctcgg > SRR3722073.269454/1‑47 (MQ=60)
|
GTCATCGAGCAGCCCTTCTGGCACATCGTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGTTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCGAGTGCAGAAGCCAGCGCCGCTTTCTTGGTTGCGCCT > NZ_CP009273/951717‑951906
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
