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 I194 R1
|
197 |
32.2 |
1845014 |
95.2% |
1756453 |
85.4 |
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%
| 68.0
/ NA
| 20 | S352P (TCG→CCG) | yheS | ABC transporter ATP‑binding protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (11/9); total (11/9) |
ATCGCATTATTCTCGACTCGATTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAATCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGAAAGGGATCAAACTCGGCTACTT > NZ_CP009273/3475618‑3475786
|
aTCGCATTATTCTCGACTCGATTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACAt > 1:194390/1‑90 (MQ=255)
aTCGCATTATTCTCGACTCGATTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACAt > 1:640736/1‑90 (MQ=255)
tCGCATTATTCTCGACTCGATTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACAtt < 2:82586/90‑1 (MQ=255)
tattCTCGACTCGATTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCaa < 1:323335/90‑1 (MQ=255)
gactcgaTTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTa > 1:781327/1‑90 (MQ=255)
ttAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTg < 1:4422/90‑1 (MQ=255)
gAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACa > 2:828654/1‑61 (MQ=255)
gAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACa < 1:828654/61‑1 (MQ=255)
gAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTgc > 2:689886/1‑90 (MQ=255)
aCCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTgcgc > 2:283333/1‑90 (MQ=255)
gTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTc < 2:400386/90‑1 (MQ=255)
gTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTc > 2:579891/1‑90 (MQ=255)
gTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTc < 1:364971/90‑1 (MQ=255)
cccGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGc > 1:621339/1‑90 (MQ=255)
ggCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGt < 1:877956/90‑1 (MQ=255)
tGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGa > 1:546375/1‑90 (MQ=255)
tGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGa > 2:170363/1‑90 (MQ=255)
tAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGAAAg < 1:362524/90‑1 (MQ=255)
ccGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGAAAGGGAt > 1:461895/1‑90 (MQ=255)
tAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGAAAGGGATCAAACTCGGCTACtt < 1:916963/90‑1 (MQ=255)
|
ATCGCATTATTCTCGACTCGATTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAATCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGAAAGGGATCAAACTCGGCTACTT > NZ_CP009273/3475618‑3475786
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 32 ≤ 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
GGCTATGGCGATCGCATTATTCTCGACTCGATTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAATCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGAAAGGGATCAAACTCGGCTACTTCGCCCAGCAT > NZ_CP009273/3475608‑3475796
|
GGCTATGGCGATCGCATTATTCTCGACTCGATTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACAT > SRR3722072.197751/1‑100 (MQ=60)
GGCTATGGCGATCGCATTATTCTCGACTCGATTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACAT > SRR3722072.652165/1‑100 (MQ=60)
TGGCGATCGCATTATTCTCGACTCGATTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATC < SRR3722072.482162/100‑1 (MQ=60)
agatgtgtataagagacagCGATTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAAC < SRR3722072.843032/81‑1 (MQ=60)
CATTATTCTCGACTCGATTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTA > SRR3722072.795029/1‑100 (MQ=60)
TATTCTCGACTCGATTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCC < SRR3722072.328991/100‑1 (MQ=60)
TTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCC < SRR3722072.4523/100‑1 (MQ=60)
AAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCctgtctcttatacacatctccgagccca > SRR3722072.472102/1‑72 (MQ=60)
GAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGC > SRR3722072.632428/1‑100 (MQ=60)
GTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAA < SRR3722072.371446/100‑1 (MQ=60)
GGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTC < SRR3722072.893077/100‑1 (MQ=60)
CGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGA > SRR3722072.556205/1‑100 (MQ=60)
GTCTGTTAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGAAAGGGAT > SRR3722072.470354/1‑100 (MQ=60)
TAGGCCGCAATGGCGCGGGTAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGAAAGGGATCAAACT < SRR3722072.368957/100‑1 (MQ=60)
TAAACCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGAAAGGGATCAAACTCGGCTACTTCGCCCAGCAT < SRR3722072.932718/100‑1 (MQ=60)
|
GGCTATGGCGATCGCATTATTCTCGACTCGATTAAACTGAACCTGGTGCCCGGCTCGCGTATTGGTCTGTTAGGCCGCAATGGCGCGGGTAAATCGACATTAATCAAACTGTTAGCCGGTGAACTTGCGCCAGTCAGCGGTGAAATTGGTCTGGCGAAAGGGATCAAACTCGGCTACTTCGCCCAGCAT > NZ_CP009273/3475608‑3475796
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ 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: ‑ |
