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 I230 R1
|
226 |
18.8 |
1048726 |
96.7% |
1014118 |
86.4 |
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 | 100.0%
| 58.5
/ NA
| 19 | Y185H (TAT→CAT) | yihS | sulfoquinovose isomerase |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (10/9); total (10/9) |
TGATTATTTCTGGCGACGTCGTGGATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATAAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTACTCTTCGGTTTTGCTGAAGGCTTCGTCCCA > NZ_CP009273/4064479‑4064645
|
cgATTATTTCTGGCGACGTCGTGGATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACa < 2:241877/89‑1 (MQ=255)
ttCTGGCGACGTCGTGGATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGa < 1:336246/90‑1 (MQ=255)
cTGGCGACGTCGTGGACAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGaaa < 1:116855/90‑1 (MQ=255)
tGGCGACGTCGTGGATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGAAAg > 2:10735/1‑90 (MQ=255)
aaTCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGAAAGCTTCCACCGCGTGCat > 2:169495/1‑90 (MQ=255)
aTCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGAAAGCTTCCACCGCGTGCata > 1:257599/1‑90 (MQ=255)
gAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGCGACGTCATGAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCa > 2:229007/1‑90 (MQ=255)
aCGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGAAAGCTTCCAc > 2:422465/1‑68 (MQ=255)
aCGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGAAAGCTTCCAc < 1:422465/68‑1 (MQ=255)
aCGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTgccg > 2:319729/1‑90 (MQ=255)
gAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCACGAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCcgccgc > 1:163024/1‑90 (MQ=255)
aTCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCgg > 1:342970/1‑90 (MQ=255)
aTCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCgg < 2:342970/90‑1 (MQ=255)
tttttGTCGTGAGTGACGTCATGAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTgcc > 2:280376/1‑65 (MQ=255)
tttttGTCGTGAGTGACGTCATGAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTgcc < 1:280376/65‑1 (MQ=255)
tttttGTCGTGAGTGACGTCATGAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTACTCTTCGGTTTTGCTg > 1:451492/1‑90 (MQ=255)
tttGTCGTGAGTGACGTCATGAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTACTCTTCGGTTTTGCTGaa < 2:451492/90‑1 (MQ=255)
gaCGTCATGAACAATCAAGAAAGCTTCCAGCGCGTGCATATTGGCATTGCCGCCGCGGTACTCTTCGGTTTTGCTGAAGGCTTCGTCCCa < 2:190496/90‑1 (MQ=255)
gaCGTCATGAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTACTCTTCGGTTTTGCTGAAGGCTTCGTCCCa < 1:180466/90‑1 (MQ=255)
|
TGATTATTTCTGGCGACGTCGTGGATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATAAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTACTCTTCGGTTTTGCTGAAGGCTTCGTCCCA > NZ_CP009273/4064479‑4064645
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 30 ≤ 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
TAATGATTATTTCTGGCGACGTCGTGGATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATAAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTACTCTTCGGTTTTGCTGAAGGCTTCGTCCCAGGATTCCAGGCACATC > NZ_CP009273/4064476‑4064661
|
TAATGATTATTTCTGGCGACGTCGTGGATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGA < SRR3722114.411749/100‑1 (MQ=60)
TTCTGGCGACGTCGTGGATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGAAAGCTTCCAC < SRR3722114.340023/100‑1 (MQ=60)
CTGGCGACGTCGTGGACAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGAAAGCTTCCACCG < SRR3722114.118094/100‑1 (MQ=60)
tataagagacagCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGAAAGCTTCCACCGCGTGCATA < SRR3722114.427645/88‑1 (MQ=60)
GTCGTGGATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGAAAGCTTCCACCGCGTGCATA > SRR3722114.260185/1‑100 (MQ=60)
GAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCACGAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGC > SRR3722114.164645/1‑100 (MQ=60)
AGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGG > SRR3722114.346869/1‑100 (MQ=60)
gtgtataagagacaGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTAC < SRR3722114.283321/86‑1 (MQ=60)
ATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTACTCTTCGGTTTTGCTG > SRR3722114.457119/1‑100 (MQ=60)
GACGTCATGAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTACTCTTCGGTTTTGCTGAAGGCTTCGTCCCAGGATTCCAGG < SRR3722114.182247/100‑1 (MQ=60)
ATGAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTACTCTTCGGTTTTGCTGAAGGCTTCGTCCCAGGATTCCAGGCACATC < SRR3722114.527946/100‑1 (MQ=60)
|
TAATGATTATTTCTGGCGACGTCGTGGATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATAAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTACTCTTCGGTTTTGCTGAAGGCTTCGTCCCAGGATTCCAGGCACATC > NZ_CP009273/4064476‑4064661
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
