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 |
1,878,490 |
T→C |
pseudogene (1082/1482 nt) |
yeaV → |
BCCT family transporter YeaV |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,878,490 | 0 | T | C | 93.0%
| 131.3
/ 2.4
| 43 | pseudogene (1082/1482 nt) | yeaV | BCCT family transporter YeaV |
| Reads supporting (aligned to +/- strand): ref base T (2/1); new base C (19/21); total (21/22) |
| Fisher's exact test for biased strand distribution p-value = 6.07e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01 |
ACGTCCCACAGGTGCTGGAAACACTGGGCGGCGAAACAGCTGTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTTCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCATATGGATGCAGTGGCCTACACCATGGCGGCGACC > NZ_CP009273/1878409‑1878569
|
aCGTCCCACAGGTGCTGGAAACACTGGGCGGCGAAACAGCTGTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTcgccg > 2:251441/1‑90 (MQ=255)
cGTCCCACAGGTGCTGGAAACACTGGGCGGCGAAACAGCTGTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTcgccgc < 1:54635/90‑1 (MQ=255)
cGTCCCACAGGTGCTGGAAACACTGGGCGGCGAAACAGCTGTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTcgccgc < 2:765789/90‑1 (MQ=255)
gTCCCACAGGTGCTGGAAACACTGGGCGGCGAAACAGCTGTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCa < 1:388069/90‑1 (MQ=255)
ccACAGGTGCTGGAAACACTGGGCGGCGAAACAGCTGTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATAc > 1:394999/1‑90 (MQ=255)
ccACAGGTGCTGGAAACACTGGGCGGCGAAACAGCTGTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATAc > 2:111974/1‑90 (MQ=255)
acaGGTGCTGGAAACACTGGGCGGCGAAACAGCTGTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCt > 1:413556/1‑90 (MQ=255)
gCTGGAAACACTGGGCGGCGAAACAGCTGTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGt > 1:341296/1‑90 (MQ=255)
gCTGGAAACACTGGGCGGCGAAACAGCTGTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGt > 2:441096/1‑90 (MQ=255)
gCTGGAAACACTGGGCGGCGAAACAGCTGTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGt > 1:486304/1‑90 (MQ=255)
gCTGGAAACACTGGGCGGCGAAACAGCTGTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGt < 1:816170/90‑1 (MQ=255)
gAAACACTGGGCGGCGAAACAGCTGTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGtgatg < 2:739600/90‑1 (MQ=255)
gAAACACTGGGCGGCGAAACAGCTGTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGtgatg < 2:786280/90‑1 (MQ=255)
gggCGGCGAAACAGCTGTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTTCCTCGCCGCATACCTGGGCGTGATGATTAtttt > 1:872599/1‑90 (MQ=255)
ggcggcGAAACAGCTGTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTc > 2:44849/1‑90 (MQ=255)
gcgAAACAGCTGTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTg > 1:620022/1‑90 (MQ=255)
gcgAAACAGCTGTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTg > 2:549815/1‑90 (MQ=255)
aaCAGCTGTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTc < 2:295973/90‑1 (MQ=255)
aaCAGCTGTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTc < 2:4457/90‑1 (MQ=255)
aaCAGCTGTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTc < 1:744162/90‑1 (MQ=255)
aaCAGCTGTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTc < 1:703271/90‑1 (MQ=255)
gTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCATATg < 1:441096/90‑1 (MQ=255)
aCAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCATATGGa > 2:286733/1‑90 (MQ=255)
cAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCATATGGAt < 1:286733/90‑1 (MQ=255)
gCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTTCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCATATGGATGc < 2:872599/90‑1 (MQ=255)
gCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCATATGGATGc < 2:413556/90‑1 (MQ=255)
gCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTG‑TCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCATATGGATGCa > 2:710583/1‑90 (MQ=255)
aaGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTcgc > 1:649865/1‑40 (MQ=255)
aaGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTcgc < 2:649865/40‑1 (MQ=255)
aaGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCATATGGATGCAg > 2:698603/1‑90 (MQ=255)
aaGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCATATGGATGCAg < 2:816098/90‑1 (MQ=255)
aaGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCATATGGATGCAg < 1:598789/90‑1 (MQ=255)
ttCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCATATGGATGCAg > 1:849192/1‑87 (MQ=255)
ttCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCATATGGATGCAg < 2:849192/87‑1 (MQ=255)
ttCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCATATGGATGCAGTgg < 2:173696/90‑1 (MQ=255)
ttCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCATATGGATGCAGTgg > 1:113950/1‑90 (MQ=255)
ttCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCATATGGATGCAGTgg > 1:135036/1‑90 (MQ=255)
cTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCATATGGATGCAGTGGcc < 1:857501/90‑1 (MQ=255)
tGTAGTTGCCAGCCGGTAAATTGTCCCTCGCCGCCTCCCTGGGCGTGATGATTATTCTCCTTGCCTCGCATATGGATGCAGTGGCCTaca < 2:639277/90‑1 (MQ=255)
gCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCATATGGATGCAg > 2:6025/1‑70 (MQ=255)
gCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCATATGGATGCAg < 1:6025/70‑1 (MQ=255)
gCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCATATGGATGCAGTGGCCTACACCATGgcggcg > 2:759569/1‑90 (MQ=255)
ggTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCATATGGATGCAGTGGCCTACACCATGGCGGCGAcc > 2:244597/1‑90 (MQ=255)
|
ACGTCCCACAGGTGCTGGAAACACTGGGCGGCGAAACAGCTGTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTTCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCATATGGATGCAGTGGCCTACACCATGGCGGCGACC > NZ_CP009273/1878409‑1878569
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 31 ≤ 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
AATCAACGTCCCACAGGTGCTGGAAACACTGGGCGGCGAAACAGCTGTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTTCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCATATGGATGCAGTGGCCTACACCATGG > NZ_CP009273/1878404‑1878561
|
AATCAACGTCCCACAGGTGCTGGAAACACTGGGCGGCGAAACAGCTGTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATAC > SRR3722072.402117/1‑100 (MQ=60)
TCAACGTCCCACAGGTGCTGGAAACACTGGGCGGCGAAACAGCTGTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCT > SRR3722072.421045/1‑100 (MQ=60)
CGTCCCACAGGTGCTGGAAACACTGGGCGGCGAAACAGCTGTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGC < SRR3722072.55626/100‑1 (MQ=60)
GTCCCACAGGTGCTGGAAACACTGGGCGGCGAAACAGCTGTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCG < SRR3722072.395018/100‑1 (MQ=60)
TCCCACAGGTGCTGGAAACACTGGGCGGCGAAACAGCTGTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGT > SRR3722072.347309/1‑100 (MQ=60)
TCCCACAGGTGCTGGAAACACTGGGCGGCGAAACAGCTGTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGT > SRR3722072.495105/1‑100 (MQ=60)
GCTGGAAACACTGGGCGGCGAAACAGCTGTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATT < SRR3722072.830385/100‑1 (MQ=60)
TGGAAACACTGGGCGGCGAAACAGCTGTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTTCCTCGCCGCATACCTGGGCGTGATGATTATTTT > SRR3722072.887624/1‑100 (MQ=60)
ACACTGGGCGGCGAAACAGCTGTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTG > SRR3722072.631086/1‑100 (MQ=60)
AACAGCTGTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCATATGGAT < SRR3722072.757329/100‑1 (MQ=60)
AACAGCTGTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCATATGGAT < SRR3722072.715819/100‑1 (MQ=60)
GCTGTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGctgtctcttatacacatctccgagcccacgagacgtccga > SRR3722072.661468/1‑60 (MQ=60)
GTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCATATGGATGCAGTGG > SRR3722072.137452/1‑100 (MQ=60)
GTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCATATGGATGCAGTGG > SRR3722072.863872/1‑100 (MQ=60)
GTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCATATGGATGCAGTGG < SRR3722072.449160/100‑1 (MQ=60)
GTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCATATGGATGCAGTGG > SRR3722072.116044/1‑100 (MQ=60)
CAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCATATGGATGCAGTGGCCT < SRR3722072.291666/100‑1 (MQ=60)
taagagacagGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCATATGGATGCAGTGGCCTACAC < SRR3722072.6149/90‑1 (MQ=60)
AAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCATATGGATGCAGTGGCCTACAC < SRR3722072.609470/100‑1 (MQ=60)
CTGATGTCGTTGCCAGCCGGTAAATTGTCCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCATATGGATGCAGTGGCCTACACCATGG < SRR3722072.872306/100‑1 (MQ=60)
|
AATCAACGTCCCACAGGTGCTGGAAACACTGGGCGGCGAAACAGCTGTACAGCAAGTTCTGATGTCGTTGCCAGCCGGTAAATTGTTCCTCGCCGCATACCTGGGCGTGATGATTATTTTCCTTGCCTCGCATATGGATGCAGTGGCCTACACCATGG > NZ_CP009273/1878404‑1878561
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
