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 I228 R1
|
214 |
26.5 |
1448192 |
97.1% |
1406194 |
86.4 |
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%
| 91.8
/ NA
| 28 | pseudogene (408/1482 nt) | yeaV | BCCT family transporter YeaV |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (14/14); total (14/14) |
GGCCTCATTAATCATGGCTTATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTTCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGGCGCACTGACCATTTCCCT > NZ_CP009273/1877729‑1877893
|
ggCCTCATTAATCATGGCTTATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCg > 1:323350/1‑90 (MQ=255)
ggCCTCATTAATCATGGCTTATCACTTTCATGCGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCg > 2:559708/1‑90 (MQ=255)
ccTCATTAATCATGGCTTATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGcc < 2:151420/90‑1 (MQ=255)
tAATCATGGCTTATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAg < 1:347331/90‑1 (MQ=255)
tAATCATGGCTTATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAg < 2:113890/90‑1 (MQ=255)
ggCTTATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATg > 1:78812/1‑90 (MQ=255)
tATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCAt > 1:381937/1‑85 (MQ=255)
tATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCAt < 2:381937/85‑1 (MQ=255)
tttCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTg > 2:215219/1‑90 (MQ=255)
tCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGt < 2:247347/90‑1 (MQ=255)
gCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGAttt > 2:426379/1‑90 (MQ=255)
gAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGAt < 2:376472/90‑1 (MQ=255)
aCAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTcc < 2:323350/90‑1 (MQ=255)
aaGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGa < 1:23959/90‑1 (MQ=255)
ggTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATc > 1:655880/1‑90 (MQ=255)
ggTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATc < 1:553995/90‑1 (MQ=255)
tGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCa > 1:158582/1‑90 (MQ=255)
tttCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCg > 2:230244/1‑90 (MQ=255)
ttCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCgg < 2:260014/90‑1 (MQ=255)
attattGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGcc > 1:261629/1‑75 (MQ=255)
attattGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGcc < 2:261629/75‑1 (MQ=255)
attGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATCTGATGTTCCTGATCGCCACTGTCGGCGCACTGAcc < 2:278156/90‑1 (MQ=255)
tgctATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGGCGCACTGACCATTTc > 1:201961/1‑90 (MQ=255)
tATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGGCGCACTGACCATTTCCCt > 1:344351/1‑90 (MQ=255)
tACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGGCGCACTGACCAtt < 2:216338/82‑1 (MQ=255)
tACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGGCGCACTGACCAtt > 1:216338/1‑82 (MQ=255)
gCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTg > 1:631828/1‑50 (MQ=255)
gCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTg < 2:631828/50‑1 (MQ=255)
|
GGCCTCATTAATCATGGCTTATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTTCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGGCGCACTGACCATTTCCCT > NZ_CP009273/1877729‑1877893
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CTTATACGCTGGCCTCATTAATCATGGCTTATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTTCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGGCGCACTGACCATTTCCCTTGTTGTTA > NZ_CP009273/1877719‑1877901
|
CTTATACGCTGGCCTCATTAATCATGGCTTATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCG > SRR3722112.327166/1‑100 (MQ=60)
CATTAATCATGGCTTATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATG > SRR3722112.79769/1‑100 (MQ=60)
TAATCATGGCTTATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGG < SRR3722112.351674/100‑1 (MQ=60)
AATCATGGCTTATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGA > SRR3722112.386897/1‑100 (MQ=60)
GAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATC > SRR3722112.666114/1‑100 (MQ=60)
AACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCA > SRR3722112.160527/1‑100 (MQ=60)
AAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGT < SRR3722112.24260/100‑1 (MQ=60)
GGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCG < SRR3722112.562384/100‑1 (MQ=60)
CCTTTCCGGCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGGCGCtgtc > SRR3722112.264704/1‑96 (MQ=60)
GCATTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGGCGCACTGACCATTTC > SRR3722112.204418/1‑100 (MQ=60)
TTATTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGGCGCACTGACCATTTCCCT > SRR3722112.348639/1‑100 (MQ=60)
TTGCTGCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGGCGCACTGACCATTTCCCTTGT > SRR3722112.218943/1‑100 (MQ=60)
GCTATTACCGGCGTCCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGctgtctcttatacacatctgacgctgccga > SRR3722112.641604/1‑70 (MQ=60)
|
CTTATACGCTGGCCTCATTAATCATGGCTTATCACTTTCATGTGCGGAAAAACAAAGGTCTGAGCCTTTCCGGCATTATTGCTGCTATTACCGGCGTTCGCCCGCAAGGCCCATGGGGAAAACTGGTCGATTTGATGTTCCTGATCGCCACTGTCGGCGCACTGACCATTTCCCTTGTTGTTA > NZ_CP009273/1877719‑1877901
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
