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 I199 R1
|
220 |
57.5 |
3163680 |
97.0% |
3068769 |
86.1 |
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 | . | 80.6%
| 77.2
/ 30.6
| 36 | intergenic (+454/‑89) | putP/BW25113_RS05295 | sodium/proline symporter PutP/FTR1 family protein |
| Reads supporting (aligned to +/- strand): ref base T (7/0); new base . (18/11); total (25/11) |
| Fisher's exact test for biased strand distribution p-value = 7.56e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.73e-01 |
CCCTGGAATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTGTTTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGAAAAACGTTTAAGGGTGGGT > NZ_CP009273/1076641‑1076808
|
cccTGGAATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTGTTTTTCtt > 1:175307/1‑90 (MQ=255)
cTGGAATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTGttttctt > 2:1405554/1‑84 (MQ=255)
cTGGAATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTGttttctt < 1:1405554/87‑4 (MQ=255)
cTGGAATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGc > 2:1270568/1‑90 (MQ=255)
cTGGAATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGc > 1:186022/1‑90 (MQ=255)
tGGAATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGcc > 2:1017970/1‑90 (MQ=255)
ggAATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCg > 1:1418033/1‑90 (MQ=255)
aatCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTGTTTTTCTTTGCCGTAAt > 2:1075947/1‑90 (MQ=255)
aatCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATg < 2:1453115/90‑1 (MQ=255)
gTTTATATCCCTTGGCATTCCCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATaa < 1:1100388/90‑1 (MQ=255)
ttGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTaa < 2:427694/73‑1 (MQ=255)
ttGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTaa > 1:427694/1‑73 (MQ=255)
ttGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACt > 1:1374507/1‑90 (MQ=255)
ttGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACt > 2:707820/1‑90 (MQ=255)
ttGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACt > 1:1216666/1‑90 (MQ=255)
ttGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACt > 1:87185/1‑90 (MQ=255)
ttGGCATTACCTCGCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGGGTTTTTCTTTGCCGTAATGATAATCGCTATCAc > 1:978762/1‑90 (MQ=255)
cATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGa < 1:84898/90‑1 (MQ=255)
tACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGAttt > 2:765133/1‑90 (MQ=255)
ctctTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTGTTTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACtt > 1:749644/1‑90 (MQ=255)
tctTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACtttt > 1:110740/1‑90 (MQ=255)
tctTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACtttt > 2:565242/1‑90 (MQ=255)
tctTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACtttt > 1:279118/1‑90 (MQ=255)
tttGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCt < 2:110740/90‑1 (MQ=255)
gTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTGTTTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCttt > 1:483540/1‑90 (MQ=255)
gTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTg > 2:310932/1‑90 (MQ=255)
tACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCAt < 1:751722/90‑1 (MQ=255)
aCATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATa > 2:1074171/1‑90 (MQ=255)
tCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGAtt < 2:770452/90‑1 (MQ=255)
cAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGa < 1:453595/90‑1 (MQ=255)
tcatTTTATAAACATTCCGCTTGTGTTTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCa > 1:163163/1‑90 (MQ=255)
tcatTTTATAAACATTCCGCTTGTGTTTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCa > 1:1323176/1‑90 (MQ=255)
tcatTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAg > 2:273920/1‑90 (MQ=255)
ttATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGaaaaa < 1:596190/90‑1 (MQ=255)
ttATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGaaaaa < 2:87185/90‑1 (MQ=255)
ttCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGAAAAACGTTTAAgg > 1:983467/1‑90 (MQ=255)
ttCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGAAAAACGTTTAAgg > 1:204862/1‑90 (MQ=255)
ttGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGAAAAACGTTTAAgggtgggt < 1:1229723/90‑1 (MQ=255)
|
CCCTGGAATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTGTTTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGAAAAACGTTTAAGGGTGGGT > NZ_CP009273/1076641‑1076808
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CATCTTTCTACCCTGGAATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTGTTTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGAAAAACGTTTAAGGGTGGGTGGCATGTTTGT > NZ_CP009273/1076631‑1076819
|
CATCTTTCTACCCTGGAATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTGTTTTTCTT > SRR3722078.177359/1‑100 (MQ=60)
TCTTTCTACCCTGGAATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGC > SRR3722078.188236/1‑100 (MQ=60)
TTTCTACCCTGGAATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCG > SRR3722078.1441065/1‑100 (MQ=60)
ACCCTGGAATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATG < SRR3722078.1428342/100‑1 (MQ=60)
GTTTATATCCCTTGGCATTCCCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCAC < SRR3722078.1117154/100‑1 (MQ=60)
TTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCctgtctc > SRR3722078.432846/1‑93 (MQ=60)
TTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACT > SRR3722078.1235793/1‑100 (MQ=60)
TTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACT > SRR3722078.88212/1‑100 (MQ=60)
TTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACT > SRR3722078.1396660/1‑100 (MQ=60)
TTTATATCCCTTGGCATTACCTCGCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGGGTTTTTCTTTGCCGTAATGATAATCGCTATCAC > SRR3722078.992851/1‑100 (MQ=60)
GGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTGTTTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTT > SRR3722078.759204/1‑100 (MQ=60)
GCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTT > SRR3722078.282528/1‑100 (MQ=60)
GCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTT > SRR3722078.112049/1‑100 (MQ=60)
CATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTC < SRR3722078.85895/100‑1 (MQ=60)
ACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTGTTTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTT > SRR3722078.489279/1‑100 (MQ=60)
TACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTC < SRR3722078.761333/100‑1 (MQ=60)
CATTCCAACATCATTTTATAAACATTCCGCTTGTGTTTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCA > SRR3722078.165063/1‑100 (MQ=60)
CATTCCAACATCATTTTATAAACATTCCGCTTGTGTTTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCA > SRR3722078.1344327/1‑100 (MQ=60)
CAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGAAAAA < SRR3722078.459015/100‑1 (MQ=60)
TTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGAAAAACGTTTAAGG > SRR3722078.997682/1‑100 (MQ=60)
TTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGAAAAACGTTTAAGG > SRR3722078.207333/1‑100 (MQ=60)
TTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGAAAAACGTTTAAGGG < SRR3722078.603104/100‑1 (MQ=60)
TTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGAAAAACGTTTAAGGGTGGGTGGCA > SRR3722078.399577/1‑100 (MQ=60)
TTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGAAAAACGTTTAAGGGTGGGTGGCATGTTTG < SRR3722078.1249099/100‑1 (MQ=60)
TGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGAAAAACGTTTAAGGGTGGGTGGCATGTTTGT > SRR3722078.1316187/1‑100 (MQ=60)
|
CATCTTTCTACCCTGGAATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTGTTTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGAAAAACGTTTAAGGGTGGGTGGCATGTTTGT > NZ_CP009273/1076631‑1076819
|
| 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: ‑ |
