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 |
1,076,727 |
(T)5→4 |
intergenic (+458/‑85) |
putP → / → BW25113_RS05295 |
sodium/proline symporter PutP/FTR1 family protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,076,723 | 0 | T | . | 96.5%
| 109.6
/ ‑2.9
| 29 | intergenic (+454/‑89) | putP/BW25113_RS05295 | sodium/proline symporter PutP/FTR1 family protein |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base . (15/13); total (15/14) |
| Fisher's exact test for biased strand distribution p-value = 4.83e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TTTCTACCCTGGAATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTGTTTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGAAAAACGTTTAAGGGTGGGT > NZ_CP009273/1076635‑1076808
|
tttCTACCCTGGAATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTGtt > 2:321869/1‑90 (MQ=255)
tCTACCCTGGAATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTGtttt > 2:592372/1‑90 (MQ=255)
cccTGGAATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTGttttcttt < 1:801561/90‑5 (MQ=255)
ccTGGAATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTg > 2:450461/1‑90 (MQ=255)
cTGGAATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACAGTCCGCTTGTG‑TTTTCTTTGc > 2:896736/1‑90 (MQ=255)
ataatCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTaa < 2:129430/90‑1 (MQ=255)
ataatCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTAAAAACATTCCGCTTGTG‑TTTTCTTTGCCGTaa < 1:528142/90‑1 (MQ=255)
aatCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATg > 2:120698/1‑90 (MQ=255)
aatCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATg > 2:254282/1‑90 (MQ=255)
tttATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAAt > 1:406056/1‑90 (MQ=255)
cccTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATc < 1:418424/90‑1 (MQ=255)
cTTGGCATTAGCTCTCTTTGTTTACATTCCAACTTCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATTAc > 2:7347/1‑90 (MQ=255)
cTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCAc > 1:595399/1‑90 (MQ=255)
ttGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACt > 2:118324/1‑90 (MQ=255)
ttGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACt < 1:268193/90‑1 (MQ=255)
ttGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGAGAATCGCTATCACt > 1:718081/1‑90 (MQ=255)
tGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTg < 1:370065/90‑1 (MQ=255)
tACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGAttt < 2:678091/90‑1 (MQ=255)
tttACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACtt > 1:764782/1‑82 (MQ=255)
tttACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACtt < 2:764782/82‑1 (MQ=255)
aTTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCAt > 1:611303/1‑87 (MQ=255)
aTTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCAt < 2:611303/87‑1 (MQ=255)
cAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGa > 2:156717/1‑90 (MQ=255)
aCATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACt < 1:450461/90‑1 (MQ=255)
atTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGa < 1:884214/59‑1 (MQ=255)
atTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGa > 2:884214/1‑59 (MQ=255)
atTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGaa > 2:859764/1‑90 (MQ=255)
ttATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGaaaaa < 2:344526/90‑1 (MQ=255)
aTTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGAAAAACGTTTAAg > 1:707343/1‑90 (MQ=255)
ccGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGAAAAACGTTTAAgggt < 1:441503/90‑1 (MQ=255)
ccGCTTGT‑TTTTTCTTTGACCTAATGATAATCGCTATCACTGCGATTTGCTTTTTTTTGCATAGATTGACTCAGAAAAACGTTTAAgggt < 2:326577/90‑1 (MQ=255)
ttGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGAAAAACGTTTAAgggtgggt < 1:838824/90‑1 (MQ=255)
|
TTTCTACCCTGGAATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTGTTTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGAAAAACGTTTAAGGGTGGGT > NZ_CP009273/1076635‑1076808
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 30 ≤ 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
TCCCATCTTTCTACCCTGGAATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTGTTTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGAAAAACGTTTAAGGGTGGGTGGCATGTTTGTTC > NZ_CP009273/1076628‑1076821
|
acgtctcgtgggctcggagatgtgtataagagacagCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTGTTTTC < SRR3722072.431051/64‑1 (MQ=60)
CCCTGGAATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGA < SRR3722072.815563/100‑1 (MQ=60)
GGAATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAAT > SRR3722072.413390/1‑100 (MQ=60)
ATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTAAAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGC < SRR3722072.537655/100‑1 (MQ=60)
GTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCAC > SRR3722072.606018/1‑100 (MQ=60)
TTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGAGAATCGCTATCACT > SRR3722072.730859/1‑100 (MQ=60)
CCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTT < SRR3722072.426010/100‑1 (MQ=60)
TTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACT < SRR3722072.272756/100‑1 (MQ=60)
TGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTT < SRR3722072.376641/100‑1 (MQ=60)
ggagatgtgtataagagacagTTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTC < SRR3722072.899434/79‑1 (MQ=60)
CCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGC > SRR3722072.778260/1‑100 (MQ=60)
CTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGA > SRR3722072.622202/1‑100 (MQ=60)
ACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGAAAAACG < SRR3722072.458709/100‑1 (MQ=60)
TTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGAAAAACGTTTAAG > SRR3722072.719955/1‑100 (MQ=60)
CCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGAAAAACGTTTAAGGGTGGGTGGCATG < SRR3722072.449575/100‑1 (MQ=60)
TTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGAAAAACGTTTAAGGGTGGGTGGCATGTTTG < SRR3722072.853360/100‑1 (MQ=60)
tgTTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGAAAAACGTTTAAGGGTGGGTGGCATGTTTGTTC < SRR3722072.466902/98‑1 (MQ=60)
|
TCCCATCTTTCTACCCTGGAATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTGTTTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGAAAAACGTTTAAGGGTGGGTGGCATGTTTGTTC > NZ_CP009273/1076628‑1076821
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
