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 I215 R1
|
7 |
24.6 |
1459714 |
95.1% |
1388188 |
84.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| JC |
NZ_CP009273 |
4,609,810 |
Δ72 bp |
coding (391‑462/1224 nt) |
deoB → |
phosphopentomutase |
|
| |
seq id |
position |
reads (cov) |
reads (cov) |
score |
skew |
freq |
annotation |
gene |
product |
| * |
? |
NZ_CP009273 |
= 4609809 | 1 (0.040) | 29 (1.260) |
19/156 |
0.2 |
96.8% |
coding (390/1224 nt) |
deoB |
phosphopentomutase |
| ? | NZ_CP009273 |
4609882 = |
1 (0.040) | coding (463/1224 nt) |
deoB |
phosphopentomutase |
GTCTGGTCACTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGAT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ > NZ_CP009273/4609716‑4609809
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ctggatCAACTGGGCGAAGAGCACATGAAAACCGGCAAGCCGATTTTCTATACCTCCGCTGACTCCGTGTTCCAGATTGCCTGCCATGAAGAA > NZ_CP009273/4609882‑4609968
GTCTGGTCACTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCT > 1:143136/1‑90
GTCTGGTCACTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCT > 2:79127/1‑90
GTCACTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATC > 1:68349/1‑90
CTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACT > 1:251863/1‑90
CTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACT > 2:597082/1‑90
CTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACT < 1:599207/90‑1
TTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGGCGAAG < 2:168273/90‑1
TTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGGCGAAG < 1:597082/90‑1
TTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGGCGAAG < 2:632516/90‑1
TGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGGCGAAGA > 1:323319/1‑90
GTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGGCGAAGAGCACA > 2:40278/1‑90
TCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGGCGAAGAGCACATGAAAACCGG > 1:549956/1‑90
GTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGGCGAAGAGCACATGAAAACCGGCAAGCCGAT < 2:725700/90‑1
GGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGGCGAAGAGCACATGAAAACCGGCAAGCCGATTT > 1:380710/1‑90
GGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGGCGAAGAGCACATGAAAACCGGCAAGCCGATTT > 1:138185/1‑90
GGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGGCGAAGAGCACATGAAAACCGGCAAGCCGATTTTC > 2:303744/1‑90
ATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGGCGAAGAGCACATGAAAACCGGCAAGCCGATTTTCTATA > 1:46474/1‑90
TCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGGCGAAGAGCACATGAAAACCGGCAAGCCGATTTTCTATACCT < 1:19625/90‑1
TCTCCGATCACGAAAACAGCTTCCCCCCAGAGCTGCTGGATCACCTGGGCGAAGAGCCCATGAAAACCGGCAAGCCGATTTTCTATACCT < 1:721912/90‑1
CCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGGCGAAGAGCACATGAAAACCGGCAAGCCGATTTTCTATACCTCCG > 1:706572/1‑90
CCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGGCGAAGAGCACATGAAAACCGGCAAGCCGATTTTCTATACCTCCG > 2:668656/1‑90
CGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGGCGAAGAGCACATGAAAACCGGCAAGCCGATTTTCTATACCTCCGC < 1:40278/90‑1
ATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGGCGAAGAGCACATGAAAACCGGCAAGCCGATTTTCTATACCTCCGCTG < 1:264860/90‑1
CGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGGCGAAGAGCACATGAAAACCGGCAAGCCGATTTTCTATACCTCCGCTGACTC < 2:191245/90‑1
AAAACAGCTTCCCGCAAGAGCTTCTGCATCAACTGGGCGAAGAGCACATGAAAACCGGCAAGCCGATTTTCTATACCTCCGCTGACTCCG < 2:351056/90‑1
AAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGGCGAAGAGCACATGAAAACCGGCAAGCCGATTTTCTATACCTCCGCTGACTCCG < 2:253830/90‑1
AAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGGCGAAGAGCACATGAAAACCGGCAAGCCGATTTTCTATACCTCCGCTGACTCCG < 1:79127/90‑1
AAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGGCGAAGAGCACATGAAAACCGGCAAGCCGATTTTCTATACCTCCGCTGACTCCG < 1:242546/90‑1
AAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGGCGAAGAGCACATGAAAACCGGCAAGCCGATTTTCTATACCTCCGCTGACTCCG < 2:95493/90‑1
TTCCCGCAAGAGCTGCTGGATCAACTGGGCGAAGAGCACATGAAAACCGGCAAGCCGATTTTCTATACCTCCGCTGACTCCGTGTTCCAG > 2:687066/1‑90
AGCTGCTGGATCAACTGGGCGAAGAGCACATGAAAACCGGCAAGCCGATTTTCTATACCTCCGCTGACTCCGTGTTCCAGATTGCCTGCC < 1:65859/90‑1
GATCAACTGGGCGAAGAGCACATGAAAACCGGCAAGCCGATTTTCTATACCTCCGCTGACTCCGTGTTCCAGATTGCCTGCCATGAAGAA < 2:416100/90‑1
GTCTGGTCACTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGAT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ > NZ_CP009273/4609716‑4609809
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ctggatCAACTGGGCGAAGAGCACATGAAAACCGGCAAGCCGATTTTCTATACCTCCGCTGACTCCGTGTTCCAGATTGCCTGCCATGAAGAA > NZ_CP009273/4609882‑4609968
|
| 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: ‑ |
| Reads not counted as support for junction |
|---|
| read_name Not counted due to insufficient overlap past the breakpoint. |
| read_name Not counted due to not crossing MOB target site duplication. |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ACCCCGTCTGGTCACTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATAAACTGGTCGAACGCGCTAATCTGCCGGGTTACCTCGGTAACTGCCACTCTT > NZ_CP009273/4609711‑4609861
|
ACCCCGTCTGGTCACTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATC > SRR3722098.69313/1‑100 (MQ=60)
GCGTCTGGTCACTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAAC < SRR3722098.651858/100‑1 (MQ=60)
CCGTCTGGTCACTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAAC < SRR3722098.671881/100‑1 (MQ=60)
CGTCTGGTCACTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACT > SRR3722098.255506/1‑100 (MQ=60)
ACTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGgcgaaga > SRR3722098.327823/1‑93 (MQ=60)
CTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGgcgaagag < SRR3722098.609291/100‑9 (MQ=60)
TTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGgcgaagagcacatgaa < SRR3722098.607121/100‑17 (MQ=60)
GTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGgcgaagagcacatgaaaaccgg > SRR3722098.559032/1‑78 (MQ=60)
CTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGgcgaagagcacatgaaaaccggcaagccgattt > SRR3722098.140233/1‑67 (MQ=60)
CTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGgcgaagagcacatgaaaaccggcaagccgattt > SRR3722098.386357/1‑67 (MQ=60)
GAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGgcgaagagcacatgaaaaccggcaagccgattttctata > SRR3722098.47110/1‑61 (MQ=60)
GGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGG > SRR3722098.718506/1‑55 (MQ=60)
GGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATAAACTGGTCGAACGCGCTAATCTGCCGGGTTACCTCGGTAACTGCCACTCTT > SRR3722098.272315/1‑100 (MQ=60)
TCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGG < SRR3722098.19900/48‑1 (MQ=60)
CGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGG < SRR3722098.40850/44‑1 (MQ=60)
ATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGG < SRR3722098.268660/42‑1 (MQ=60)
AAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGG < SRR3722098.246084/36‑1 (MQ=60)
AAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGG < SRR3722098.80227/36‑1 (MQ=60)
|
ACCCCGTCTGGTCACTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATAAACTGGTCGAACGCGCTAATCTGCCGGGTTACCTCGGTAACTGCCACTCTT > NZ_CP009273/4609711‑4609861
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
