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 |
2,753,169 |
T→C |
S276P (TCA→CCA) |
yfjI → |
YfjI family protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,753,169 | 0 | T | C | 100.0%
| 77.4
/ NA
| 22 | S276P (TCA→CCA) | yfjI | YfjI family protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (12/10); total (12/10) |
CAAAGGGGATTGGATTTTTTGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAA‑TTTCCAACCCAATTTTTTCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCATTAAAATTAATG > NZ_CP009273/2753083‑2753241
|
cAAAGGGGATTGGATTTTTTGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAA‑TTTCCAACCCAATTTTTCCaa > 2:40408/1‑90 (MQ=255)
attggattTTTTGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAA‑TTTCCAACCCAATTTTTCCAAATGAACAt > 2:723453/1‑90 (MQ=255)
attggattTTTTGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAA‑TTTCCAACCCAATTTTTCCAAATGAACAt > 1:549138/1‑90 (MQ=255)
aCGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAA‑TTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCa > 1:307908/1‑90 (MQ=255)
gTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAA‑TTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCa > 2:869128/1‑90 (MQ=255)
tGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAA‑TTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCaa < 1:497188/90‑1 (MQ=255)
tGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAA‑TTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCaa < 2:549138/90‑1 (MQ=255)
gCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCaa < 1:92089/90‑1 (MQ=255)
tgCCAGCCTGCTTCAACACAAGGTAACAGAAAAA‑TTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCaa < 1:243558/81‑1 (MQ=255)
tgCCAGCCTGCTTCAACACAAGGTAACAGAAAAA‑TTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCaa > 2:243558/1‑81 (MQ=255)
tgCCAGCCTGCTTCAACACAAGGTAACAGAAAAA‑TTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATg > 1:920131/1‑90 (MQ=255)
tgCCAGCCTGCTTCAACACAAGGTAACAGAAAAA‑TTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATg > 1:525402/1‑90 (MQ=255)
ccAGCCTGCTTCAACACAAGGTAACAGAAAAA‑TTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGa > 1:761816/1‑90 (MQ=255)
gCCTGCTTCAACACAAGGTAACAGAAAAA‑TTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAAt > 2:187602/1‑90 (MQ=255)
caAGGTAACAGAAAAA‑TTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGc < 1:599605/90‑1 (MQ=255)
aaGGTAACAGAAAAA‑TTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGca < 1:905721/90‑1 (MQ=255)
tAACAGAAAAA‑TTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGcatcat > 1:779667/1‑90 (MQ=255)
aaCAGAAAAA‑TTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCAtt < 1:678398/90‑1 (MQ=255)
aCAGAAAAA‑TTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCATTa > 1:72927/1‑90 (MQ=255)
tttCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCATTAAAATTAATg < 2:235036/90‑1 (MQ=255)
tttCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCATTAAAATTAATg < 1:723453/90‑1 (MQ=255)
tttCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCATTAAAATTAATg < 1:110956/90‑1 (MQ=255)
|
CAAAGGGGATTGGATTTTTTGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAA‑TTTCCAACCCAATTTTTTCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCATTAAAATTAATG > NZ_CP009273/2753083‑2753241
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GGCAAAGGGGATTGGATTTTTTGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAA‑TTTCCAACCCAATTTTTTCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCATTAAAATTAATGAAAATAATCG > NZ_CP009273/2753081‑2753251
|
GGCAAAGGGGATTGGATTTTTTGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAA‑TTTCCAACCCAATTTTTCCAAATGAACAT > SRR3722072.559018/1‑100 (MQ=60)
GATTTTTTGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAA‑TTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCA > SRR3722072.313251/1‑100 (MQ=60)
GTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAA‑TTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATG > SRR3722072.534852/1‑100 (MQ=60)
GTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAA‑TTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATG > SRR3722072.935929/1‑100 (MQ=60)
TGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAA‑TTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGG < SRR3722072.247645/100‑1 (MQ=60)
TGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAA‑TTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGG < SRR3722072.506164/100‑1 (MQ=60)
GCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGG < SRR3722072.93784/100‑1 (MQ=60)
GCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAA‑TTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGA > SRR3722072.775244/1‑100 (MQ=60)
CAACACAAGGTAACAGAAAAA‑TTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCAT > SRR3722072.793351/1‑100 (MQ=60)
ACACAAGGTAACAGAAAAA‑TTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCATTA > SRR3722072.74284/1‑100 (MQ=60)
CAAGGTAACAGAAAAA‑TTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCATTAAAA < SRR3722072.610302/100‑1 (MQ=60)
AAGGTAACAGAAAAA‑TTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCATTAAAAT < SRR3722072.921309/100‑1 (MQ=60)
AACAGAAAAA‑TTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCATTAAAATTAATG < SRR3722072.690535/100‑1 (MQ=60)
TTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCATTAAAATTAATGAAAATAATCG < SRR3722072.113009/100‑1 (MQ=60)
TTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCATTAAAATTAATGAAAATAATCG < SRR3722072.736310/100‑1 (MQ=60)
|
GGCAAAGGGGATTGGATTTTTTGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAA‑TTTCCAACCCAATTTTTTCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCATTAAAATTAATGAAAATAATCG > NZ_CP009273/2753081‑2753251
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
