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 I207 R1
|
218 |
45.0 |
2482936 |
97.1% |
2410930 |
86.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,054,234 |
A→G |
E232G (GAA→GGA) |
torC → |
pentaheme c‑type cytochrome TorC |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,054,234 | 0 | A | G | 96.2%
| 81.9
/ NA
| 26 | E232G (GAA→GGA) | torC | pentaheme c‑type cytochrome TorC |
| Reads supporting (aligned to +/- strand): ref base A (1/0); new base G (14/11); total (15/11) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CGCTGTACTCTATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGAAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGTCAGCGTGTACT > NZ_CP009273/1054153‑1054318
|
cGCTGTACTCTATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAg < 2:806702/90‑1 (MQ=255)
cGCTGTACTCTATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAg < 1:280284/90‑1 (MQ=255)
cGCTGTACTCTATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAg < 1:740980/90‑1 (MQ=255)
tGTACTCTATTGATATTAAGCCAATTTATACGGCGAAAGGCGATAAAGAAGCCTCTGCTTCTCTGCCCCCTGCTTCGGAAGCGAAACTcc > 1:506435/1‑90 (MQ=255)
gTACTCTATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCt > 1:662763/1‑90 (MQ=255)
tATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACg > 1:108947/1‑90 (MQ=255)
tATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACg > 2:1062081/1‑90 (MQ=255)
aTTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGt > 2:1051944/1‑90 (MQ=255)
gATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAg > 1:1060530/1‑76 (MQ=255)
gATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAg < 2:1060530/76‑1 (MQ=255)
gATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGAc > 2:137107/1‑90 (MQ=255)
tatTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGACgg > 2:638864/1‑90 (MQ=255)
tAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGACGGCGa > 1:511660/1‑90 (MQ=255)
aaGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGACGGCGAc > 2:1177225/1‑90 (MQ=255)
aGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGACGGCGACt < 2:19326/90‑1 (MQ=255)
tGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAAt > 2:420132/1‑90 (MQ=255)
gcggcgAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAAtt > 1:716173/1‑90 (MQ=255)
gATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGc > 1:71815/1‑90 (MQ=255)
gCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGaa > 1:159837/1‑90 (MQ=255)
tGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAgcgc < 1:908054/90‑1 (MQ=255)
tGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAgcgc < 1:397414/90‑1 (MQ=255)
tGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAgcgc < 1:345765/90‑1 (MQ=255)
ctctGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGAc > 2:58080/1‑90 (MQ=255)
tgctgcCTGCTTCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGTc < 2:159837/90‑1 (MQ=255)
gcctgcTTCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGTCAGCg < 2:662763/90‑1 (MQ=255)
ttCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGTCAGCGTGTACt < 1:1020845/90‑1 (MQ=255)
|
CGCTGTACTCTATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGAAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGTCAGCGTGTACT > NZ_CP009273/1054153‑1054318
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ 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
TGGTGACACGCTGTACTCTATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGAAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGTCAGCGTGTACTCACCCAATTCCCAGG > NZ_CP009273/1054145‑1054333
|
TGGTGACACGCTGTACTCTATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTC < SRR3722089.629390/100‑1 (MQ=60)
GGTGACACGCTGTACTCTATTGATATTAAGCCAATTTATACGGCGAAAGGCGATAAAGAAGCCTCTGCTTCTCTGCCCCCTGCTTCGGAAGCGAAACTCC > SRR3722089.512409/1‑100 (MQ=60)
GTGACACGCTGTACTCTATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCT > SRR3722089.671309/1‑100 (MQ=60)
CGCTGTACTCTATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACG > SRR3722089.110284/1‑100 (MQ=60)
CGCTGTACTCTATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACG < SRR3722089.283865/100‑1 (MQ=60)
CGCTGTACTCTATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACG < SRR3722089.750695/100‑1 (MQ=60)
GTACTCTATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGctgt > SRR3722089.1076445/1‑96 (MQ=60)
CTATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGACGGCGA > SRR3722089.517684/1‑100 (MQ=60)
GCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATT > SRR3722089.725482/1‑100 (MQ=60)
GGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGC > SRR3722089.72689/1‑100 (MQ=60)
CGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAA > SRR3722089.161827/1‑100 (MQ=60)
TGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGTCAG < SRR3722089.350066/100‑1 (MQ=60)
TGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGTCAG < SRR3722089.402249/100‑1 (MQ=60)
TGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGTCAG < SRR3722089.921254/100‑1 (MQ=60)
TTCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGTCAGCGTGTACTCACCCAATTC < SRR3722089.1036060/100‑1 (MQ=60)
GAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGTCAGCGTGTACTCACCCAATTCCCAGG < SRR3722089.1137156/100‑1 (MQ=60)
|
TGGTGACACGCTGTACTCTATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGAAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGTCAGCGTGTACTCACCCAATTCCCAGG > NZ_CP009273/1054145‑1054333
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
