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 I200 R1
|
216 |
30.8 |
1683622 |
97.2% |
1636480 |
87.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,934,547 |
T→C |
intergenic (‑97/+23) |
lpxM ← / ← mepM |
lauroyl‑Kdo(2)‑lipid IV(A) myristoyltransferase/murein DD‑endopeptidase MepM |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,934,547 | 0 | T | C | 92.9%
| 34.4
/ ‑3.1
| 14 | intergenic (‑97/+23) | lpxM/mepM | lauroyl‑Kdo(2)‑lipid IV(A) myristoyltransferase/murein DD‑endopeptidase MepM |
| Reads supporting (aligned to +/- strand): ref base T (1/0); new base C (8/5); total (9/5) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.57e-01 |
TTCGGATAAGGCAAAAATCAATCTGGTGATAGTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGTACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCACAATCTCTTTGGCCTGCGCCAGGAATTCGCGACGATCGGAGCCG > NZ_CP009273/1934462‑1934636
|
ttCGGATAAGGCAAAAATCAATCTGGTGATAGTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCg > 1:521017/1‑90 (MQ=255)
ggATAAGGCAAAAATCAATCTGGTGATAGTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGTACCGGCt > 1:243550/1‑90 (MQ=255)
aGGCAAAAATCAATCTGGTGATAGTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGaa > 1:490075/1‑90 (MQ=255)
ggCAAAAATCAATCTGGTGATAGTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAAt < 2:376141/90‑1 (MQ=255)
caatcTGGTGATAGTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGttaa < 1:72549/90‑1 (MQ=255)
ggTGATAGTGTAGCGGCGCAACTTGTCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATc < 1:234260/90‑1 (MQ=255)
gtgtAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGt > 2:21459/1‑90 (MQ=255)
tgtAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTa < 1:631489/90‑1 (MQ=255)
gcgcAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCgg > 1:415600/1‑90 (MQ=255)
gcAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGca > 2:15153/1‑90 (MQ=255)
aaCTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGcaca < 2:521017/90‑1 (MQ=255)
gCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGGAGCTGCGGCACAATCTCTTTgg > 2:152661/1‑90 (MQ=255)
aaaTAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCACAATCTCTTTGGCCTgc > 2:437612/1‑90 (MQ=255)
aaaaaaGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCGAACCGTAGCTGCGGCACAATCTCTTTGGCCTGCGCCAg > 2:319787/1‑90 (MQ=255)
tACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCACAATCTCTTTGGCCTGCGCCAGGAATTCGCGACGATCGGAGCCg > 1:780117/1‑90 (MQ=255)
|
TTCGGATAAGGCAAAAATCAATCTGGTGATAGTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGTACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCACAATCTCTTTGGCCTGCGCCAGGAATTCGCGACGATCGGAGCCG > NZ_CP009273/1934462‑1934636
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ATGCTTTTCCAGTTTCGGATAAGGCAAAAATCAATCTGGTGATAGTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGTACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCACAATCTCTTTGGCCTGCGCCAGGAATTCGCGACGATCGGAGCCG > NZ_CP009273/1934449‑1934636
|
ATGCTTTTCCAGTTTCGGATAAGGCAAAAATCAATCTGGTGATAGTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCA < SRR3722079.766110/100‑1 (MQ=60)
TGCTTTTCCAGTTTCGGATAAGGCAAAAATCAATCTGGTGATAGTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGTAC < SRR3722079.744866/100‑1 (MQ=60)
CTTTTCCAGTTTCGGATAAGGCAAAAATCAATCTGGTGATAGTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCG > SRR3722079.525827/1‑100 (MQ=60)
tctcgtgggctcggagatgtgtataagagacagGGTGATAGTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGG < SRR3722079.239778/67‑1 (MQ=60)
TTTTCCAGTTTCGGATAAGGCAAAAATCAATCTGGTGATAGTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGG < SRR3722079.164628/100‑1 (MQ=60)
TTCCAGTTTCGGATAAGGCAAAAATCAATCTGGTGATAGTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGTACCGGCT > SRR3722079.245602/1‑100 (MQ=60)
GTTTCGGATAAGGCAAAAATCAATCTGGTGATAGTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAA > SRR3722079.494384/1‑100 (MQ=60)
CAATCTGGTGATAGTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAAC < SRR3722079.73153/100‑1 (MQ=60)
GGTGATAGTGTAGCGGCGCAACTTGTCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGC < SRR3722079.236243/100‑1 (MQ=60)
TAGTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGG > SRR3722079.419172/1‑100 (MQ=60)
TGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGCACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCAC < SRR3722079.637946/100‑1 (MQ=60)
ACTGACTGCGTACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCACAATCTCTTTGGCCTGCGCCAGGAATTCGCGACGATCGGAGCCG > SRR3722079.788478/1‑100 (MQ=60)
|
ATGCTTTTCCAGTTTCGGATAAGGCAAAAATCAATCTGGTGATAGTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTGACTGCGTACCGGCTGCGAATGGATGTTAATTAATCAAACCGTAGCTGCGGCACAATCTCTTTGGCCTGCGCCAGGAATTCGCGACGATCGGAGCCG > NZ_CP009273/1934449‑1934636
|
| 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: ‑ |
