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 I227 R1
|
223 |
21.3 |
1167702 |
97.0% |
1132670 |
86.4 |
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%
| 55.4
/ NA
| 18 | S276P (TCA→CCA) | yfjI | YfjI family protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (8/10); total (8/10) |
AAAGGGGATTGGATTTTTTGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTTCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCATTAAAATT > NZ_CP009273/2753084‑2753237
|
aaaGGGGATTGGATTTTTTGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCaaa < 2:182192/90‑1 (MQ=255)
gattggattTTTTGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACa > 2:520070/1‑90 (MQ=255)
gattggattTTTTGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACa > 1:361903/1‑90 (MQ=255)
attggattTTTTGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACAt > 2:281769/1‑90 (MQ=255)
attTTTTGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGcc < 2:441428/90‑1 (MQ=255)
ttttttGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCg < 2:406042/90‑1 (MQ=255)
tGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCaa < 2:93456/90‑1 (MQ=255)
tGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCaa < 2:135375/90‑1 (MQ=255)
tgCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGt < 2:308318/71‑1 (MQ=255)
tgCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGt > 1:308318/1‑71 (MQ=255)
tgCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATg > 2:245517/1‑90 (MQ=255)
tgCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATg > 1:23703/1‑90 (MQ=255)
tgCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATg > 1:135702/1‑90 (MQ=255)
gCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAAt < 2:135702/90‑1 (MQ=255)
gCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAAt < 1:213856/90‑1 (MQ=255)
tGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTCCCGGTATTTCACCAACGTCTTATGGAAATTGt < 1:513557/90‑1 (MQ=255)
caAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGc < 2:252044/90‑1 (MQ=255)
aaaaTTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCATTAAAAtt > 1:440890/1‑90 (MQ=255)
|
AAAGGGGATTGGATTTTTTGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTTCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCATTAAAATT > NZ_CP009273/2753084‑2753237
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ 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
TGGCAAAGGGGATTGGATTTTTTGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTTCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCATTAAAATT > NZ_CP009273/2753080‑2753237
|
TGGCAAAGGGGATTGGATTTTTTGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACA > SRR3722111.366949/1‑100 (MQ=60)
GGCAAAGGGGATTGGATTTTTTGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACAT < SRR3722111.590346/100‑1 (MQ=60)
GTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACtgtctctt > SRR3722111.312341/1‑92 (MQ=60)
GTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATG > SRR3722111.137412/1‑100 (MQ=60)
GTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATG > SRR3722111.23994/1‑100 (MQ=60)
GCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAG < SRR3722111.216461/100‑1 (MQ=60)
TGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTCCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGC < SRR3722111.521545/100‑1 (MQ=60)
AGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCATTAAAATT > SRR3722111.447521/1‑100 (MQ=60)
|
TGGCAAAGGGGATTGGATTTTTTGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTTCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCATTAAAATT > NZ_CP009273/2753080‑2753237
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
