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 I195 R1
|
222 |
27.1 |
1551108 |
96.0% |
1489063 |
86.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,934,995 |
+C |
intergenic (‑308/‑173) |
yieP ← / → BW25113_RS19520 |
FadR/GntR family transcriptional regulator/16S ribosomal RNA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,934,991 | 1 | . | C | 86.2%
| 73.6
/ 7.7
| 29 | intergenic (‑304/‑177) | yieP/BW25113_RS19520 | FadR/GntR family transcriptional regulator/16S ribosomal RNA |
| Reads supporting (aligned to +/- strand): ref base . (1/3); new base C (10/15); total (11/18) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.89e-01 |
CCGCCGGGTCAGCGGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCA‑C‑A‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGAT > NZ_CP009273/3934902‑3935075
|
ccgccgGGTCAGCGGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGca‑c‑a > 2:764148/1‑90 (MQ=33)
tGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCA‑C‑ACCCCCGCGCCGCTGAGAAaaagc < 2:736933/90‑1 (MQ=255)
aCTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCA‑C‑ACCCCCGCGCCGCTGAGAAaaagcaaagc < 1:508199/90‑1 (MQ=255)
aCTCCGGCAGAGAAAGCAAAAATAAATGCTTGACCCTGTAGCGGGAAAGCGTATTATGCA‑C‑ACCCCCGCGCCGCTGAGAAaaagcaaagc < 2:504092/90‑1 (MQ=11)
ccGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCA‑CAA‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGc > 1:339002/1‑90 (MQ=255)
ccGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCA‑C‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGc > 1:361678/1‑90 (MQ=255)
gCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCA‑C‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACt < 2:473355/90‑1 (MQ=255)
gCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCA‑C‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACt < 2:164336/90‑1 (MQ=255)
cAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCA‑C‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAAc < 1:631795/90‑1 (MQ=255)
aaaaTAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACC‑C‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACaa < 1:699790/90‑1 (MQ=11)
aaaaTAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCA‑C‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACaa < 2:361678/90‑1 (MQ=255)
aaaaTAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCA‑C‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACaa < 2:339002/90‑1 (MQ=255)
taaatGCTTGACTCTGTAGCGGGAAAGCGTATTATGCA‑C‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTa < 1:604763/90‑1 (MQ=255)
aatGCTTGACTCTGTAGCGGGAAAGCGTATTATGCA‑C‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATc > 1:704536/1‑90 (MQ=255)
tGCTTGACTCTGTAGCGGGAAAGCGTATTATGCA‑CGC‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAg < 2:244982/90‑1 (MQ=11)
cTTGACTCTGTAGCGGGAAAGCGTATTATGCA‑C‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGAc < 1:759506/90‑1 (MQ=255)
tGACTCTGTAGCGGGAAAGCGTATTATGCACC‑C‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACaa < 1:432136/90‑1 (MQ=11)
ctctGTAGCTGGAAAGCGTATTATGCA‑C‑ACCCCCCCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCt < 1:402017/90‑1 (MQ=11)
tctGTAGCGGGAAAGCGTATTATGCA‑C‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCtg > 2:310514/1‑90 (MQ=255)
gTAGCGGGAAAGCGTATTATGCA‑C‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCtgtgt > 1:10915/1‑90 (MQ=255)
gTAGCGGGAAAGCGTATTATGCA‑C‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCtgtgt > 2:285542/1‑90 (MQ=255)
cGGGAAAGCGTATTATGCA‑C‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGc < 1:457423/90‑1 (MQ=255)
cGGGAAAGCGTATTATGCA‑C‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGc < 2:270231/90‑1 (MQ=255)
gggAAAGCGTATTATGCA‑C‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACt < 2:254748/54‑1 (MQ=14)
gggAAAGCGTATTATGCA‑C‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACt > 1:254748/1‑54 (MQ=14)
gggAAAGCGTATTATGCA‑C‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCa > 1:358262/1‑90 (MQ=255)
aGCGTATTATGCA‑C‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGa > 2:240048/1‑90 (MQ=255)
gTATTATGCA‑C‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGa > 1:148477/1‑90 (MQ=255)
ttatGCA‑C‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGAGGGCACTCGAAGATAc < 1:403166/90‑1 (MQ=11)
gCA‑C‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGAt > 2:350374/1‑90 (MQ=255)
|
CCGCCGGGTCAGCGGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCA‑C‑A‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGAT > NZ_CP009273/3934902‑3935075
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
AACACGCCGCCGGGTCAGCGGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCA‑C‑A‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAACG > NZ_CP009273/3934896‑3935083
|
AACACGCCGCCGGGTCAGCGGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCA‑C‑A‑CCCC < SRR3722073.263463/100‑1 (MQ=8)
AACACGCCGCCGGGTCAGCGGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCA‑C‑A‑CCCC < SRR3722073.375153/100‑1 (MQ=8)
cgagatctacacactgcatatcgtcggcagcgtcagatgtgtataagagacagGCTTGACTCTGTAGCGGGAAAGCGTATTATGCA‑C‑ACCCCCGCGCCGC < SRR3722073.533514/47‑1 (MQ=20)
CTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCA‑C‑A‑CCCCctgtctcttatacacatctgacgct > SRR3722073.656387/1‑75 (MQ=10)
CCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCA‑CAA‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGC > SRR3722073.346200/1‑100 (MQ=24)
CCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCA‑C‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGC > SRR3722073.369346/1‑100 (MQ=24)
ACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCA‑C‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTC < SRR3722073.518917/100‑1 (MQ=24)
AGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCA‑C‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATC > SRR3722073.718797/1‑100 (MQ=24)
CAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCA‑C‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAG < SRR3722073.644869/100‑1 (MQ=24)
AAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACC‑C‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGAC < SRR3722073.713987/100‑1 (MQ=23)
TAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCA‑C‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATC < SRR3722073.617352/100‑1 (MQ=24)
GCTTGACTCTGTAGCGGGAAAGCGTATTATGCA‑C‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGT > SRR3722073.11196/1‑100 (MQ=24)
CTTGACTCTGTAGCGGGAAAGCGTATTATGCA‑C‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTG < SRR3722073.774850/100‑1 (MQ=24)
TGACTCTGTAGCGGGAAAGCGTATTATGCACC‑C‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGG < SRR3722073.441383/100‑1 (MQ=23)
ACTCTGTAGCGGGAAAGCGTATTATGCA‑C‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACctgtctcttatacacatctgacgctg > SRR3722073.260098/1‑74 (MQ=27)
ACTCTGTAGCGGGAAAGCGTATTATGCA‑C‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCA > SRR3722073.365846/1‑100 (MQ=24)
CTCTGTAGCTGGAAAGCGTATTATGCA‑C‑ACCCCCCCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCAC < SRR3722073.410586/100‑1 (MQ=22)
GCGGGAAAGCGTATTATGCA‑C‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGA > SRR3722073.151529/1‑100 (MQ=24)
CGGGAAAGCGTATTATGCA‑C‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGAT < SRR3722073.467188/100‑1 (MQ=24)
GCGTATTATGCA‑C‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATT > SRR3722073.728700/1‑100 (MQ=6)
TATTATGCA‑C‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTT > SRR3722073.445827/1‑100 (MQ=6)
ATTATGCA‑C‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTA > SRR3722073.293796/1‑100 (MQ=6)
TTATGCA‑C‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGAGGGCACTCGAAGATACGGATTCTTAA < SRR3722073.411763/100‑1 (MQ=5)
ATGCA‑C‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAACG > SRR3722073.143482/1‑100 (MQ=6)
|
AACACGCCGCCGGGTCAGCGGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCA‑C‑A‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAACG > NZ_CP009273/3934896‑3935083
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
