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 |
4,064,564 |
A→G |
Y185H (TAT→CAT) |
yihS ← |
sulfoquinovose isomerase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,064,564 | 0 | A | G | 76.9%
| 15.7
/ 3.6
| 13 | Y185H (TAT→CAT) | yihS | sulfoquinovose isomerase |
| Reads supporting (aligned to +/- strand): ref base A (1/2); new base G (6/4); total (7/6) |
| Fisher's exact test for biased strand distribution p-value = 5.59e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.55e-01 |
TATTTCTGGCGACGTCGTGGATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATAAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTACTCTTCGGTTTTGCTGAAGGCTTCGTCCCAGGAT > NZ_CP009273/4064483‑4064649
|
tattTCTGGCGACGTCGTGGATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCa > 2:307974/1‑90 (MQ=255)
tttCTGGCGACGTCGTGGATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAg > 1:382505/1‑90 (MQ=255)
tttCTGGCGACGTCGTGGATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAg > 2:380585/1‑90 (MQ=255)
tttCTGGCGACGTCGTGGATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATAAACAATCAAg > 2:383429/1‑90 (MQ=255)
tGGCGACGTCGTGGATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGAAAg > 1:352169/1‑90 (MQ=255)
ggATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGAAAGCTTCCACCGCGt < 1:98700/90‑1 (MQ=255)
ggATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGAAAGCTTCCACCGCGt < 2:107529/90‑1 (MQ=255)
ggATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGAAAGCTTCCACCGCGt < 2:78118/90‑1 (MQ=255)
tCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATAAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGt < 1:224850/90‑1 (MQ=255)
tttttGTCGTGAGTGACGTCATGAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTACTCTTCGGTTTTGCTg > 1:74823/1‑90 (MQ=255)
gtgagtgaCGTCATAAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTACTCTTCGGTTTTGCTGAAGGCTTc < 1:383429/90‑1 (MQ=255)
aCGTCATGAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTACTCTTCGGTTTTGCTGAAGGCTTCGTCCCAg < 1:52448/90‑1 (MQ=255)
tCATGAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTACTCTTCGGTTTTGCTGAAGGCTTCGTCCCAGGAt > 1:412134/1‑90 (MQ=255)
|
TATTTCTGGCGACGTCGTGGATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATAAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTACTCTTCGGTTTTGCTGAAGGCTTCGTCCCAGGAT > NZ_CP009273/4064483‑4064649
|
| 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
TAACGCGATAATGATTATTTCTGGCGACGTCGTGGATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATAAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTACTCTTCGGTTTTGCTGAAGGCTTCGTCCCAGGATTCCAGGCACATC > NZ_CP009273/4064468‑4064661
|
TAACGCGATAATGATTATTTCTGGCGACGTCGTGGATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAAC < SRR3722109.409859/100‑1 (MQ=60)
ATAATGATTATTTCTGGCGACGTCGTGGATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAG > SRR3722109.387950/1‑100 (MQ=60)
TGATTATTTCTGGCGACGTCGTGGATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGAAAG > SRR3722109.356960/1‑100 (MQ=60)
GGATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGC < SRR3722109.99923/100‑1 (MQ=60)
TCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATAAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTACTCTTCGGT < SRR3722109.227528/100‑1 (MQ=60)
ATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTACTCTTCGGTTTTGCTG > SRR3722109.75727/1‑100 (MQ=60)
GTGAGTGACGTCATGAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTACTCTTCGGTTTTGCTGAAGGCTTCGTCCCAGGAT > SRR3722109.418150/1‑100 (MQ=60)
GTGAGTGACGTCATAAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTACTCTTCGGTTTTGCTGAAGGCTTCGTCCCAGGAT < SRR3722109.388889/100‑1 (MQ=60)
ACGTCATGAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTACTCTTCGGTTTTGCTGAAGGCTTCGTCCCAGGATTCCAGGC < SRR3722109.53073/100‑1 (MQ=60)
GTCATGAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTACTCTTCGGTTTTGCTGAAGGCTTCGTCCCAGGATTCCAGGCAC > SRR3722109.222372/1‑100 (MQ=60)
GTCATGAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTACTCTTCGGTTTTGCTGAAGGCTTCGTCCCAGGATTCCAGGCAC > SRR3722109.292872/1‑100 (MQ=60)
CATGAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTACTCTTCGGTTTTGCTGAAGGCTTCGTCCCAGGATTCCAGGCACAT > SRR3722109.199956/1‑100 (MQ=60)
ATGAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTACTCTTCGGTTTTGCTGAAGGCTTCGTCCCAGGATTCCAGGCACATC < SRR3722109.171369/100‑1 (MQ=60)
|
TAACGCGATAATGATTATTTCTGGCGACGTCGTGGATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATAAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTACTCTTCGGTTTTGCTGAAGGCTTCGTCCCAGGATTCCAGGCACATC > NZ_CP009273/4064468‑4064661
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
