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 |
2,713,233 |
(A)5→4 |
coding (652/699 nt) |
tapT → |
tRNA‑uridine aminocarboxypropyltransferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,713,229 | 0 | A | . | 100.0%
| 87.8
/ NA
| 22 | coding (648/699 nt) | tapT | tRNA‑uridine aminocarboxypropyltransferase |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base . (11/11); total (11/11) |
TGTTAGATATGGCCGGCGATACCGGGGCGGCGGCAGGGTTAGGCGAGCATTTTACCCGCTTTAAAACACGCTATCTGGCAGGAAAAACGCAACATCTGGGTAGCATCACAGCAGAACAGTTAGAAAGCGTTTAAAATCATTCGGTCACTTCTGCGGGAGACCGGTAT > NZ_CP009273/2713147‑2713313
|
tGTTAGATATGGCCGGCGATACCGGGGCGGCGGCAGGGTTAGGCGAGCATTTTACCCGCTTTAAAACACGCTATCTGGCAGGaaaacgca < 1:277043/90‑5 (MQ=255)
tGTTAGATATGGCCGGCGATACCGGGGCGGCGGCAGGGTTAGGCGAGCATTTTACCCGCTTTAAAACACGCTATCTGGCAGGaaaacgca < 2:124060/90‑5 (MQ=255)
gATATGGCCGGCGATACCGGGGCGGCGGCAGGGTTAGGCGAGCATTTTACCCGCTTTAAAACACGCTATCTGGCAGG‑AAAACGCAACATc > 2:65961/1‑90 (MQ=255)
tGGCCGGCGATACCGGGGCGGCGGCAGGGTTAGGCGAGCATTTTACCCGCTTTAAAACACGCTATCTGGCAGG‑AAAACGCAACATCTggg > 2:670397/1‑90 (MQ=255)
tGGCCGGCGATACCGGGGCGGCGGCAGGGTTAGGCGAGCATTTTACCCGCTTTAAAACACGCTATCTGGCAGG‑AAAACGCAACATCTggg > 2:513644/1‑90 (MQ=255)
gCCGGCGATACCGGGGCGGCGGCAGGGTTAGGCGAGCATTTTACCCGCTTTAAAACACGCTATCTGGCAGG‑AAAACGCAACATCTGGGTa > 1:255745/1‑90 (MQ=255)
gCCGGCGATACCGGGGCGGCGGCAGGGTTAGGCGAGCATTTTACCCGCTTTAAAACACGCTATCTGGCAGG‑AAAACGCAACATCTGGGTa > 2:490508/1‑90 (MQ=255)
gCCGGCGATACCGGGGCGGCGGCAGGGTTAGGCGAGCATTTTACCCGCTTTAAAACACGCTATCTGGCAGG‑AAAACGCAACATCTGGGTa < 1:65961/90‑1 (MQ=255)
cGATACCGGGGCGGCGGCAGGGTTAGGCGAGCATTTTACCCGCTTTAAAACACGCTATCTGGCAGG‑AAAACGCAACATCTGGGTAGCATc < 2:303594/90‑1 (MQ=255)
aTACCGGGGCGGCGGCAGGGTTAGGCGAGCATTTTACCCGCTTTAAAACACGCTATCTGGCAGG‑AAACCGCAACATCTGGGTAGCATcac < 2:753341/90‑1 (MQ=255)
aTACCGGGGCGGCGGCAGGGTTAGGCGAGCATTTTACCCGCTTTAAAACACGCTATCTGGCAGG‑AAAACGCAACATCTGGGTAGCATcac < 1:223958/90‑1 (MQ=255)
ccGGGGCGGCGGCAGGGTTAGGCGAGCATTTTACCCGCTTTAAAACACGCTATCTGGCAGG‑AAAACGCAACATCTGGGTAGCATCAcagc < 2:325546/90‑1 (MQ=255)
gggCGGCGGCAGGGTTAGGCGAGCATTTTACCCGCTTTAAAACACGCTATCTGGCAGG‑AAAACGCAACATCTGGGTAGCATCACAGCAGa < 2:691243/90‑1 (MQ=255)
gcggcggcAGGGTTAGGCGAGCATTTTACCCGCTTTAAAACACGCTATCTGGCAGG‑AAAACGCAACATCTGGGTAGCATCACAGCAGAAc < 1:286102/90‑1 (MQ=255)
ggcggcAGGGTTAGGCGAGCATTTTACCCGCTTTAAAACACGATATCTGGCAGG‑AAAACGCAACATCTGGGTAGCATCACAGCAGAACAg > 2:550945/1‑90 (MQ=255)
cGAGCATTTTACCCGCTTTAAAACACGCTATCTGGCAGG‑AAAACGCAACATCTGGGTAGCATc > 2:29493/1‑63 (MQ=255)
cGAGCATTTTACCCGCTTTAAAACACGCTATCTGGCAGG‑AAAACGCAACATCTGGGTAGCATc < 1:29493/63‑1 (MQ=255)
aGCATTTTACCCGCTTTAAAACACGCTATCTGGCAGG‑AAAACGCAACATCTGGGTAGCATCACAGCAGAACAGTTAGAAAGCGTTTaaaa > 2:272899/1‑90 (MQ=255)
gCATTTTACCCGCTTTAAAACACGCTATCTGGCAGG‑AAAACGCAACATCTGGGTAGCATcac < 2:372074/62‑1 (MQ=255)
gCATTTTACCCGCTTTAAAACACGCTATCTGGCAGG‑AAAACGCAACATCTGGGTAGCATcac > 1:372074/1‑62 (MQ=255)
ttACCCGCTTTAAAACACGCTATCTGGCAGG‑AAAACGCAACATCTGGGTAGCATCACAGCAGAACAGTTAGAAAGCGTTTAAAATCATTc > 2:518039/1‑90 (MQ=255)
tttAAAACACGCTATCTGGCAGG‑AAAACGCAACATCTGGGTAGCATCACAGCAGAACAGTTAGAAAGCGTTTAAAATCATTCGGTCACtt > 1:628575/1‑90 (MQ=255)
tATCTGGCAGG‑AAAACGCAACATCTGGGTAGCATCACAGCAGAACAGTTAGAAAGCGTTTAAAATCATTCGGTCACTTCTGCGGGAGAcc < 2:628575/90‑1 (MQ=255)
ggCAGG‑AAAACGCAACATCTGGGTAGCATCACAGCAGAACAGTTAGAAAGCGTTTAAAATCATTCGGTCACTTCTGCGGGAGACCGGTAt < 1:74874/90‑1 (MQ=255)
|
TGTTAGATATGGCCGGCGATACCGGGGCGGCGGCAGGGTTAGGCGAGCATTTTACCCGCTTTAAAACACGCTATCTGGCAGGAAAAACGCAACATCTGGGTAGCATCACAGCAGAACAGTTAGAAAGCGTTTAAAATCATTCGGTCACTTCTGCGGGAGACCGGTAT > NZ_CP009273/2713147‑2713313
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TGTTAGATATGGCCGGCGATACCGGGGCGGCGGCAGGGTTAGGCGAGCATTTTACCCGCTTTAAAACACGCTATCTGGCAGGAAAAACGCAACATCTGGGTAGCATCACAGCAGAACAGTTAGAAAGCGTTTAAAATCATTCGGTCACTTCTGCGGGAGACCGGTATGAGTCAGCGA > NZ_CP009273/2713147‑2713323
|
TGTTAGATATGGCCGGCGATACCGGGGCGGCGGCAGGGTTAGGCGAGCATTTTACCCGCTTTAAAACACGCTATCTGGCAGG‑AAAACGCAACATCTGGGT < SRR3722072.281779/100‑1 (MQ=60)
GTTAGATATGGCCGGCGATACCGGGGCGGCGGCAGGGTTAGGCGAGCATTTTACCCGCTTTAAAACACGCTATCTGGCAGG‑AAAACGCAACATCTGGGTA > SRR3722072.260084/1‑100 (MQ=60)
GCCGGCGATACCGGGGCGGCGGCAGGGTTAGGCGAGCATTTTACCCGCTTTAAAACACGCTATCTGGCAGG‑AAAACGCAACATCTGGGTAGCATCACAGC < SRR3722072.67179/100‑1 (MQ=60)
atgtgtataagagacaGCAGGGTTAGGCGAGCATTTTACCCGCTTTAAAACACGCTATCTGGCAGG‑AAAACGCAACATCTGGGTAGCATCACAGCAGAAC < SRR3722072.30011/84‑1 (MQ=60)
ATACCGGGGCGGCGGCAGGGTTAGGCGAGCATTTTACCCGCTTTAAAACACGCTATCTGGCAGG‑AAAACGCAACATCTGGGTAGCATCACAGCAGAACAG < SRR3722072.227748/100‑1 (MQ=60)
GCGGCGGCAGGGTTAGGCGAGCATTTTACCCGCTTTAAAACACGCTATCTGGCAGG‑AAAACGCAACATCTGGGTAGCATCACAGCAGAACAGTTAGAAAG < SRR3722072.291027/100‑1 (MQ=60)
GGTTAGGCGAGCATTTTACCCGCTTTAAAACACGCTATCTGGCAGG‑AAAACGCAACATCTGGGTAGCATCACAGCAGAACAGctgtctcttatacacatc > SRR3722072.378687/1‑82 (MQ=60)
TTTTACCCGCTTTAAAACACGCTATCTGGCAGG‑AAAACGCAACATCTGGGTAGCATCACAGCAGAACAGTTAGAAAGCGTTTAAAATCATTCGGTCACTT > SRR3722072.639797/1‑100 (MQ=60)
GGCAGG‑AAAACGCAACATCTGGGTAGCATCACAGCAGAACAGTTAGAAAGCGTTTAAAATCATTCGGTCACTTCTGCGGGAGACCGGTATGAGTCAGCGA < SRR3722072.76272/100‑1 (MQ=60)
|
TGTTAGATATGGCCGGCGATACCGGGGCGGCGGCAGGGTTAGGCGAGCATTTTACCCGCTTTAAAACACGCTATCTGGCAGGAAAAACGCAACATCTGGGTAGCATCACAGCAGAACAGTTAGAAAGCGTTTAAAATCATTCGGTCACTTCTGCGGGAGACCGGTATGAGTCAGCGA > NZ_CP009273/2713147‑2713323
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
