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 I195 R1
|
222 |
27.1 |
1551108 |
96.0% |
1489063 |
86.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,877,816 |
T→C |
pseudogene (408/1482 nt) |
yeaV → |
BCCT family transporter YeaV |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,877,816 | 0 | T | C | 100.0%
| 72.2
/ NA
| 22 | pseudogene (408/1482 nt) | yeaV | BCCT family transporter YeaV |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (11/11); total (11/11) |
GGCCTCATTAATCATGGCTTATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTTCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGGCGCACTGACCATTTCCCTTGTTGTTAC > NZ_CP009273/1877729‑1877902
|
ggCCTCATTAATCATGGCTTATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCg > 1:296430/1‑90 (MQ=255)
ggCTTATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATg > 1:392655/1‑90 (MQ=255)
ggCTTATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATg > 1:607552/1‑90 (MQ=255)
tATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGa > 2:188636/1‑90 (MQ=255)
gtgCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGAt < 2:156158/90‑1 (MQ=255)
gCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGAttt < 2:593004/90‑1 (MQ=255)
cGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTg > 2:337679/1‑90 (MQ=255)
aaaGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTg < 1:680219/90‑1 (MQ=255)
ggTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATc > 2:727123/1‑90 (MQ=255)
cTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGcc > 1:344429/1‑90 (MQ=255)
cTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGcc < 1:738669/90‑1 (MQ=255)
gAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCAc > 1:99009/1‑90 (MQ=255)
tttCCGGCCTTATTGCTGCTATTACCGGCGCCCGCCCGCAAGGCCCATGGGGTAAACTGGGCGATTTGATGTTCCTGATCGCCGCTGTCg > 1:652730/1‑90 (MQ=255)
cATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGGCGCACt < 2:194463/90‑1 (MQ=255)
attattGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGGCGCACTg < 2:344429/90‑1 (MQ=255)
attGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGGCGCACTGAcc < 1:123441/90‑1 (MQ=255)
gctgctATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGGCGCACTGACCAtt < 2:565737/90‑1 (MQ=255)
gctgctATTACCAGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGGCGCACTGACCAtt < 1:540387/90‑1 (MQ=255)
ctATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGGCGCACTGACCATTTccc > 2:228489/1‑90 (MQ=255)
tACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGa > 2:536173/1‑47 (MQ=255)
tACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGa < 1:536173/47‑1 (MQ=255)
cGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGGCGCACTGACCATTTCCCTTGTTGTTAc < 1:188636/90‑1 (MQ=255)
|
GGCCTCATTAATCATGGCTTATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTTCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGGCGCACTGACCATTTCCCTTGTTGTTAC > NZ_CP009273/1877729‑1877902
|
| 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
CTTATACGCTGGCCTCATTAATCATGGCTTATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTTCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGGCGCACTGACCATTTCCCTTGTTGTTACCGCAGCAACC > NZ_CP009273/1877719‑1877912
|
CTTATACGCTGGCCTCATTAATCATGGCTTATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCG > SRR3722073.302703/1‑100 (MQ=60)
CATTAATCATGGCTTATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATG > SRR3722073.401017/1‑100 (MQ=60)
CATTAATCATGGCTTATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATG > SRR3722073.620210/1‑100 (MQ=60)
tacacactgcatatcgtcggcagcgtcagatgtgtataagagacagACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTG < SRR3722073.201096/54‑1 (MQ=60)
tcgtcggcagcgtcagatgtgtataagagacagTTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGAT < SRR3722073.547362/67‑1 (MQ=60)
AAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCC > SRR3722073.351721/1‑100 (MQ=60)
ACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCAC > SRR3722073.101166/1‑100 (MQ=60)
AAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTG < SRR3722073.694116/100‑1 (MQ=60)
GGTCTGAGCCTTTCCGGCCTTATTGCTGCTATTACCGGCGCCCGCCCGCAAGGCCCATGGGGTAAACTGGGCGATTTGATGTTCCTGATCGCCGCTGTCG > SRR3722073.666140/1‑100 (MQ=60)
CTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGGCG < SRR3722073.753625/100‑1 (MQ=60)
ATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGGCGCACTGACCATTTCCCTTG < SRR3722073.126050/100‑1 (MQ=60)
GCTGCTATTACCAGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGGCGCACTGACCATTTCCCTTGTTG < SRR3722073.551684/100‑1 (MQ=60)
ACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGGCGCACTGACCATTTCCCTTGTTGTTACCGCAG > SRR3722073.177825/1‑100 (MQ=60)
CGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGGCGCACTGACCATTTCCCTTGTTGTTACCGCAGCAACN < SRR3722073.192362/100‑1 (MQ=60)
|
CTTATACGCTGGCCTCATTAATCATGGCTTATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTTCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGGCGCACTGACCATTTCCCTTGTTGTTACCGCAGCAACC > NZ_CP009273/1877719‑1877912
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
