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 F21 I1 R5
|
781 |
658.8 |
22969755 |
98.0% |
22510359 |
137.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP025268 |
2,997,537 |
(A)8→7 |
intergenic (‑140/+83) |
CXP41_RS15625 ← / ← CXP41_RS24400 |
response regulator transcription factor/hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP025268 | 2,997,530 | 0 | A | . | 100.0%
| 80.2
/ NA
| 18 | intergenic (‑133/+90) | CXP41_RS15625/CXP41_RS24400 | response regulator transcription factor/hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base . (8/10); total (8/10) |
TCCCATATATTCATCCTGAGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGA > NZ_CP025268/2997392‑2997649
|
tCCCATATATTCATCCTGAGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGTaa < 2:4394723/140‑1 (MQ=255)
tcctCCTGAGTGTAACTGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACCTTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACca < 1:706306/137‑1 (MQ=255)
gAGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCAt > 2:5511993/1‑140 (MQ=255)
aGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCAtt > 2:236628/1‑140 (MQ=255)
ttAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATga > 1:1586929/1‑140 (MQ=255)
cattcattTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAgatgat < 1:6281374/140‑1 (MQ=255)
tataATCATCCCTTCCATTATTATTATAAGCAAAATCCACAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAatat < 2:2560136/140‑1 (MQ=255)
tataATCATCCCTTACATTATTATTATAAGCAAAAACCAAAGAATACAATGATGAAATAATAATGAAAAATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGTCATTAAAAAATCATGAGATGATTAAAatat < 2:8496553/140‑1 (MQ=255)
ccTTCCATTATTATTATAAGCATAATCAAAATAATTCATTGTTGAAATAATAATGTAATATAATTTATAATAAAATTTTTGAGT‑AAAAAAATACAACAGGCATTAAAAAATCATGCTATGATTAAAATATTACAATTTGa < 2:5353749/140‑1 (MQ=255)
ttCCATTATTATTATAAGCAAAATCCAAAGAAGACCGTGATGAAATAATAATGAACTATAATTACAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATGAAAAAATCATGAGATGATTAAAATATTACAATTAGAtg > 2:10878424/1‑139 (MQ=255)
aGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAgg < 1:5135126/140‑1 (MQ=255)
aGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAgg < 2:8690036/140‑1 (MQ=255)
gAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAggg < 1:3062094/140‑1 (MQ=255)
aTTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCtat < 2:104830/140‑1 (MQ=255)
tgaAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTc > 1:1081155/1‑140 (MQ=255)
gAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATgag > 1:8996610/1‑63 (MQ=255)
gAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATgag < 2:8996609/63‑1 (MQ=255)
aagtataATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGcc > 2:5584470/4‑140 (MQ=255)
ttAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGa > 2:571439/1‑140 (MQ=255)
|
TCCCATATATTCATCCTGAGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGA > NZ_CP025268/2997392‑2997649
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TCATCCTGAGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTT > NZ_CP025268/2997402‑2997685
|
TCCTCCTGAGTGTAACTGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACCTTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAA < SRR14920170.712525/151‑1 (MQ=60)
GTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGA > SRR14920170.1600558/1‑151 (MQ=60)
ccccccccccccccccccccccccccccccccccccacttttcacgcagaagacggcatacgcgataggctccggtctcgtgggctcggagatgtgtataagagacagAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAAT < SRR14920170.7137625/43‑1 (MQ=60)
CATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTAC < SRR14920170.6335648/151‑1 (MQ=60)
ttttcaagcagaagacggcatacgagataggctccggtctcgtgggctcggagatgtgtataagagacagAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATC < SRR14920170.365373/81‑1 (MQ=60)
AGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGT < SRR14920170.5178835/151‑1 (MQ=60)
GAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTC > SRR14920170.1090451/1‑151 (MQ=60)
GAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTC < SRR14920170.3088359/151‑1 (MQ=60)
GAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATctgtctcttatacacatctccgagcccacgagaccggagcctatcgcgtatgccggcttatgcttg > SRR14920170.9075344/1‑85 (MQ=60)
AAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATctgtctcttatacacatctccgagcccacgagaccggagcctatctcgtatgccgtcttctgcttgaaaaggggggggggggggggggggggggggggggggggggggggg > SRR14920170.3611374/1‑40 (MQ=60)
|
TCATCCTGAGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTT > NZ_CP025268/2997402‑2997685
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
