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 F4 I96 R1
|
227 |
23.3 |
882352 |
98.0% |
864704 |
126.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
923,801 |
A→G |
V284A (GTC→GCC) |
cydC ← |
cysteine/glutathione ABC transporter ATP‑binding protein/permease CydC |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 923,801 | 0 | A | G | 87.5%
| 39.5
/ 0.3
| 16 | V284A (GTC→GCC) | cydC | cysteine/glutathione ABC transporter ATP‑binding protein/permease CydC |
| Reads supporting (aligned to +/- strand): ref base A (1/1); new base G (6/8); total (7/9) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.19e-01 |
TCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCAGAGATACGTACGGCAGAGGCAAT‑GACTTGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGACAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACGCCGCCAGACGCCATCCACAGCATCAGGATCACCGCTAACGCGCCAATGAGCAGCATTATCGCTTGCGACAATGCGGTCAGTT > NZ_CP009273/923669‑923927
|
tCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCAGAGATACGTACGGCAGAGGCAAT‑GACTTGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCaaa > 2:247550/1‑137 (MQ=255)
cTCCGGTTTTTGATCCGTTAAGTCAGAGATACGTACGGCAGAGGCAAT‑GACTTGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAAcgcg > 2:8621/1‑139 (MQ=255)
cGGTTTTTGATCCGTTAAGTCAGAGATACGTACGGCAGAGGCAAT‑GACTTGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGcc < 2:230174/138‑1 (MQ=255)
tCCGTTAAGTCAGAGATACGTACGGCAGAGGCAATGGACTTGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGACAAACAGGGCAATTAACGCGCCGGGTTGAGCa > 1:122748/1‑139 (MQ=255)
atagaTACGTACGGCAGAGGCAAT‑GACTTGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAAcg < 2:102249/137‑1 (MQ=255)
gaTACGTACGGCAGAGGCAAT‑GACTTGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAAcgcg > 1:268749/1‑112 (MQ=255)
gaTACGTACGGCAGAGGCAAT‑GACTTGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAAcgcg < 2:268749/112‑1 (MQ=255)
agGCAAT‑GACTTGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAATCGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACGCCGCCAGACGCCATCca < 2:366853/139‑1 (MQ=255)
ggCAATGGACTTGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGACAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACGCCGCCAGACGCCATCca < 2:122748/139‑1 (MQ=255)
gCAAT‑GACTTGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACGCCGCCAGACGCCATCca > 2:387171/1‑137 (MQ=255)
gATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACGCCGCCAGACGCCATCCACAGCATCAGGATCACCGc > 2:430770/1‑139 (MQ=255)
ccGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACGCCGCCAGACGCCATCCACAGCATCAGGATCACCGCTAACGCGCCAATGag < 1:8621/139‑1 (MQ=255)
cAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACGCCGCCAGACGCCATCCACAGCATCAGGATCACCGCTAACGCGCCAATGAGCAGCATTATCGCTTGCGACaa > 2:128667/1‑139 (MQ=255)
gcgGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACGCCGCCAGACGCCATCCACAGCATCAGGATCACCGCTAACGCGCCAATGAGCAGCATTATCGCTTGCGACAATGCgg < 1:387171/139‑1 (MQ=255)
gcgGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACGCCGCCAGACGCCATCCACAGCATCAGGATCACCGCTAACGCGCCAATGAGCAGCATTATCGCTTGCGACAATGCgg < 2:113754/139‑1 (MQ=255)
aCGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACGCCGCCAGACGCCATCCACAGCATCAGGATCACCGCTAACGCGCCAATGAGCAGCATTATCGCTTGCGACAATGCGGTCAGtt < 2:114612/138‑1 (MQ=255)
|
TCAGGAAAGGTGACCTCCGGTTTTTGATCCGTTAAGTCAGAGATACGTACGGCAGAGGCAAT‑GACTTGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGACAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACGCCGCCAGACGCCATCCACAGCATCAGGATCACCGCTAACGCGCCAATGAGCAGCATTATCGCTTGCGACAATGCGGTCAGTT > NZ_CP009273/923669‑923927
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CCGGTTTTTGATCCGTTAAGTCAGAGATACGTACGGCAGAGGCAAT‑GACTTGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGACAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACGCCGCCAGACGCCATCCACAGCATCAGGATCACCGCTAACGCGCCAATGAGCAGCATTATCGCTTGCGACAATGCGGTCAGTTCAGATTGACGGCGTTGCGCTTCC > NZ_CP009273/923685‑923950
|
CCGGTTTTTGATCCGTTAAGTCAGAGATACGTACGGCAGAGGCAATGGACTTGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGACAAACAGGGCAATTAACGCGCCGGGTTGAGCAT > SRR3722119.123975/1‑151 (MQ=60)
GTTAAGTCAGAGATACGTACGGCAGAGGCAAT‑GACTTGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCctgtctcttatacacat > SRR3722119.271528/1‑134 (MQ=60)
CCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACGCCGCCAGACGCCATCCACAGCATCAGGATCACCGCTAACGCGCCAATGAGCAGCATTATCG < SRR3722119.8689/151‑1 (MQ=60)
CGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACGCCGCCAGACGCCATCCACAGCATCAGGATCACCGCTAACGCGCCAATGAGCAGCATTATCGCTTGCGACAATGCGGTCAGTTCAGAT < SRR3722119.391063/151‑1 (MQ=60)
GAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACGCCGCCAGACGCCATCCACAGCATCAGGATCACCGCTAACGCGCCAATGAGCAGCATTATCGCTTGCGACAATGCGGTCAGTTCAGATTGACGGCGTTGCGCT > SRR3722119.74035/1‑151 (MQ=60)
GGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACGCCGCCAGACGCCATCCACAGCATCAGGATCACCGCTAACGCGCCAATGAGCAGCATTATCGCTTGCGACAATGCGGTCAGTTCAGATTGACGGCGTTGCGCTTCC > SRR3722119.146678/1‑151 (MQ=60)
|
CCGGTTTTTGATCCGTTAAGTCAGAGATACGTACGGCAGAGGCAAT‑GACTTGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGACAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACGCCGCCAGACGCCATCCACAGCATCAGGATCACCGCTAACGCGCCAATGAGCAGCATTATCGCTTGCGACAATGCGGTCAGTTCAGATTGACGGCGTTGCGCTTCC > NZ_CP009273/923685‑923950
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
