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 I210 R1
|
226 |
19.6 |
1130256 |
95.4% |
1078264 |
84.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,475,701 |
T→C |
S352P (TCG→CCG) |
yheS → |
ABC transporter ATP‑binding protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,475,701 | 0 | T | C | 100.0%
| 18.0
/ NA
| 7 | S352P (TCG→CCG) | yheS | ABC transporter ATP‑binding protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (3/4); total (3/4) |
CATTATTCTCGACTCGATTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAATCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGAAAGGGATCAAACTCGGCTA > NZ_CP009273/3475622‑3475783
|
cATTATTCTCGACTCGATTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAAt > 1:162258/1‑90 (MQ=255)
gactcgaTTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTa < 1:434118/90‑1 (MQ=255)
gAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTgc > 2:530997/1‑90 (MQ=255)
cccGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGc < 1:272230/90‑1 (MQ=255)
tGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCt < 2:38757/90‑1 (MQ=255)
aTGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGAAAGGGATCAAAc < 1:136493/90‑1 (MQ=255)
gggTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGAAAGGGATCAAACTCGGCTa > 1:314959/1‑90 (MQ=255)
|
CATTATTCTCGACTCGATTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAATCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGAAAGGGATCAAACTCGGCTA > NZ_CP009273/3475622‑3475783
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ 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
AGCGCGGGCTATGGCGATCGCATTATTCTCGACTCGATTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAATCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGAAAGGGATCAAACTCGGCTACTTCGCCCAGCATCAA > NZ_CP009273/3475602‑3475799
|
AGCGCGGGCTATGGCGATCGCATTATTCTCGACTCGATTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAAC < SRR3722092.333960/100‑1 (MQ=60)
ATGGCGATCGCATTATTCTCGACTCGATTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAAT > SRR3722092.164979/1‑100 (MQ=60)
GACTCGATTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAAC < SRR3722092.442592/100‑1 (MQ=60)
CCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTG < SRR3722092.276804/100‑1 (MQ=60)
GCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGAAAGGGATCAAACTCGGCTA > SRR3722092.320530/1‑100 (MQ=60)
ATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGAAAGGGATCAAACTCGGCTACTT < SRR3722092.138788/100‑1 (MQ=60)
ACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGAAAGGGATCAAACTCGGCTACTTCGCCCAGCATCAA > SRR3722092.452581/1‑100 (MQ=60)
|
AGCGCGGGCTATGGCGATCGCATTATTCTCGACTCGATTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAATCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGAAAGGGATCAAACTCGGCTACTTCGCCCAGCATCAA > NZ_CP009273/3475602‑3475799
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
