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 I225 R1
|
227 |
21.4 |
1179702 |
97.1% |
1145490 |
86.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,223,232 |
(A)8→7 |
coding (63/294 nt) |
BW25113_RS06140 → |
YcgL domain‑containing protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,223,225 | 0 | A | . | 100.0%
| 63.0
/ NA
| 16 | coding (56/294 nt) | BW25113_RS06140 | YcgL domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base . (9/7); total (9/7) |
ATGCCAAAACCTGGCATCTTAAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCGAAAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATTCTGCCGCTGG > NZ_CP009273/1223137‑1223308
|
aTGCCAAAACCTGGCATCTTAAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCGaa > 2:519604/1‑90 (MQ=255)
aTGCCAAAACCTGGCATCTTAAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCGaa > 2:182550/1‑90 (MQ=255)
tGGCATCTTAAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGAt > 2:496527/1‑90 (MQ=255)
ttAAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTcgc < 1:383677/90‑1 (MQ=255)
aaaGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCgt < 1:327472/90‑1 (MQ=255)
aTGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAAc > 1:299367/1‑90 (MQ=255)
aTGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAAc > 2:364193/1‑90 (MQ=255)
ttGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACtgatg > 1:322424/1‑90 (MQ=255)
cGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGTTc < 2:332292/90‑1 (MQ=255)
cGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTc < 1:496527/90‑1 (MQ=255)
cGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTc < 2:327276/90‑1 (MQ=255)
cGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTc < 2:31917/90‑1 (MQ=255)
gACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTc > 2:218445/1‑75 (MQ=255)
gACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTc < 1:218445/75‑1 (MQ=255)
ccAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCgatg > 2:318704/1‑90 (MQ=255)
tATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATTCTGc > 1:294928/1‑90 (MQ=255)
tatGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATTCTGCCGCTgg > 2:248846/1‑90 (MQ=255)
tatGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATTCTGCCGCTgg > 1:150804/1‑90 (MQ=255)
|
ATGCCAAAACCTGGCATCTTAAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCGAAAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATTCTGCCGCTGG > NZ_CP009273/1223137‑1223308
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ 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
TTAAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCGAAAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATTCTGCCGCTGGATGGG > NZ_CP009273/1223155‑1223313
|
TTAAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGA < SRR3722109.389139/100‑1 (MQ=60)
AAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGG < SRR3722109.331805/100‑1 (MQ=60)
GAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAAC > SRR3722109.303243/1‑100 (MQ=60)
AAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATG > SRR3722109.326680/1‑100 (MQ=60)
gacAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTT < SRR3722109.221066/97‑1 (MQ=60)
CGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTT < SRR3722109.504023/100‑1 (MQ=60)
TGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATTCTGC > SRR3722109.298727/1‑100 (MQ=60)
GACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATTCTGCCGCTGG > SRR3722109.152666/1‑100 (MQ=60)
ATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGctgtctcttatacacatctga > SRR3722109.521398/1‑79 (MQ=60)
|
TTAAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCGAAAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATTCTGCCGCTGGATGGG > NZ_CP009273/1223155‑1223313
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
