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 |
|
A6 F17 I0 R1
|
24 |
52.5 |
1051376 |
97.9% |
1029297 |
229.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_000913 |
3,862,673 |
G→A |
43.7% |
pseudogene (931/1617 nt) |
glvC ← |
pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 3,862,673 | 0 | G | A | 43.7%
| 1.4
/ 2.4
| 18 | pseudogene (931/1617 nt) | glvC | pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component |
| Reads supporting (aligned to +/- strand): ref base G (6/3); new base A (3/3); total (10/8) |
| Fisher's exact test for biased strand distribution p-value = 6.22e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACCTAGTCAATCAGACCTCCGCCCATGTTGCCCACCACACCAAAGAGATACATTACGGTCGACATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAATTCCAGCGGTTCGGTAATTCCCACCAGCATGGC‑GGTTAAGGTTGC‑GGGAATCAGCAAGCCCG‑CCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAGTACATCGCTAAAGAAAT‑GCCCACGGCACC‑AAAGATTTTTGAGTTACCGTGC‑AGGG‑C‑AAAACCGCCTTCCGGGAACAACGATTTCAGCGGCTCGGCGCTCAAACTGAACTCTTGCAGATGCTGCGCCCAGTACATCTGAATGCCGCCTTCAACAGCTGCCGGACCAAAGATAAACTGTCCGT > NC_000913/3862451‑3862897
|
tatCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACCTAGTCAATCAGACCTCCGCCCATGTTGCCCACCACACCAAAGAGATACATTACGGTCGACATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAATTCCAGCGGTTCGGTAATTCCCACCAGCATGGC‑GGTTAAGGTTGC‑GGGAAACAGCAAGCCCA‑CCA‑Ctttt > 1:135186/1‑239 (MQ=255)
gcgTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACCTAGTCAATCAGACCTCCGCCCATGTTGCCCACCACACCAAAGAGATACATTACGGTCGACATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAATTCCAGCGGTTCGGTAATTCCCACCAGCATGGC‑GGATCAGGTTGC‑GGGAATCAGCAAACCCC‑CCC‑CTTTTTccc > 1:17210/1‑238 (MQ=255)
gcgTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACCTAGTCAATCAGACCTCCGCCCATGGTGCGCACCACACCAAAGAGATACATTACGGTCGACATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAATTCCAGCGGGTCGGTAATTCCCACCAGCATGGCGGGTTAGAGTGGC‑GGGAA‑CAGCAAAgccg‑cccgcttttcacg > 2:274631/1‑228 (MQ=255)
gCTGAACATCGGGATCCAGTTTTGCGGTAAAACCTAGTCAATCAGACCTCCGCCCATGTTGCCCACCACACCAAAGAGATACATTACGGTCGACATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAATTCCAGCGGTTCGGTAATTCCCACCAGCATGGC‑GGCTAAAGGTGCTGGGAACCA‑CAAACCCG‑CCACCTTTTCCCCGATTTTcg > 2:319353/1‑238 (MQ=255)
gtggcagaaaagCCTAGTCAAACAGCCCCCCCCCCAGTTTGCCCACCACACAAAAAAGAAACATCACGGCCGACATGGGCCCCGCCGGCGCGGCTTGTACCGCAAACACCAAGGGTGAAATGAACAGGAAGGAAAATTCCGGCGGTGCGTTAACCCCCACCAGCAGGGC‑GGTTAAGGTGGG‑GGGAATCAGAAAGCCCG‑CCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAGTAc < 2:135186/228‑1 (MQ=255)
tggCGATAAAACCTAATCAACCAGCCCCCCGCCCTTGTTGCCCACCCCACAAAAGAGAAACATGACGGTCGACATGGAGGCCGCAAGACCGGGGTGTCCCGAAAACAGAAAGGGGAAAAAAAACAGGAGGGAAAATCCCAGCGGTTCGGTATTCCCCACAAGCAGGGT‑GGTTAGGGTGGG‑GGAAAACAAAAACCCCG‑CCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAGTACATCg < 2:309330/237‑1 (MQ=255)
gTCAATCAGACCTCCGCCCATGTTGCCCACCACACCAAAGAGATACATTACGGTCGACATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAATTCCAGCGGTTCGGTAATTCCCACCAGCATGGC‑GGTTTAAGTTGC‑GGGGATCAACAAACCCG‑CCC‑CCTTTTCTCCGCTTTCCGGTGCGGCCGGGGAGTACATCCCTCaaaaaactccc > 2:127945/1‑233 (MQ=255)
tACATTACGGTCGACATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAATTCCAGCGGTTCGGTAATTCCCACCAGCATGGC‑GGGTAAAGTTGC‑GGGGATCAGCAAGCCCC‑CCACCTTTTACCC‑CTTTTTCGGTGCGGCCGTGAAAGAAATCGCCAAAAAAAA‑GCCCACCGCACC‑CAAGATTTTTTTGGTACCCCGC‑CGGGCC‑AAAAccc > 2:200519/1‑237 (MQ=255)
tACGGTCGACATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAATTCCAGCGGTTCGGTAATTCCCACCAGCATGGC‑GGTTAAAGTTTC‑GGGGATAAACAAACCCC‑CCC‑CCTTTTCCCCATTTTTCCGGGCGGCAGGGGAGGACAACGCCAAAGAAATACCCCACGCCCCC‑AAAAATTTTT‑AGTTACCCTGC‑CGGG‑CAAAAACCCCCTTcc > 2:389163/1‑239 (MQ=255)
cGGTCGACATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAATTCCAGCGGTTCGGTAATTCCCACCAGCATGGC‑GGATAAGGGTGC‑GGGAATAAGCAAAACCC‑CCC‑CTTTTTTCCCATTTTTCGGGGCGGGAGTGGAGTAAATCGCCTAAGAAAA‑GACCCCGGCACCAAAAAATTTTTAAGTATCGGTGA‑GGGG‑C‑AAAAcacctcccggg > 2:20137/1‑229 (MQ=255)
cGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAATTCCAGCGGTTCGGTAATTCCCACCAGCATGGC‑GGGTAAAGTTGC‑GGGGATCAACAAACCCGCCCC‑CTTTTCCCCGATTTT‑CGGGGCGGGCGGGAAGGAAAACGCTAAAGAAAA‑ACCCCCGGCACC‑AAAGAATTTTTAGGTACCGTGCAAGGG‑C‑AAAACGCCCTCCCGGCAAAAAC‑ATTTTAACGGCTCGgcggc > 2:266821/1‑236 (MQ=255)
acAAACAGAAAGGGGAAAAAGAACAGGAAGTTAATTCCGCGGGGTTGGGTAATCCCCCCCAGGAGGGG‑GGTTAGGGTGGG‑GGAAAAAAACAAGCCCG‑CCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAGTACATCGCTAAAGAAAT‑GCCCACGGCACC‑AAAGATTTTTGAGTTACCGTGC‑AGGG‑C‑AAAACCGCCTTCCGGGAACAACGATTTCAGCGGCTCGGCGCTCAAACTGaa < 2:17210/238‑1 (MQ=255)
aCAGCAACGGTGAAATGAACAGGAAGGTAAATTCCAGCGGTTCGGTAATTCCCACCAGCATGGC‑GGTTAAGGGTGC‑GGGGATCAGCAAGCCCG‑CCA‑CTTTTACCCGATTTTTCGGTGCGGCAGTGGAGTACATCGCTAAAGAAAA‑GCCCACGGGCCC‑AAAGAATTTTGTGGTACCGTGC‑CGGG‑C‑ACAACCGCCTTCCCGGaa > 1:395678/1‑202 (MQ=255)
ccaccaGGGC‑GGTTAAGGTTGC‑GGAAATGAGCAAGCCCG‑CCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAGTACATCGCTAAAGAAAT‑GCCCACGGCACC‑AAAGATTTTTGAGTTACCGTGC‑AGGG‑C‑AAAACCGCCTTCCGGGAACAACGATTTCAGCGGCTCGGCGCTCAAACTGAACTCTTGCAGATGCTGCGCCCAGTACATCTGAATGCCGCCTTCAACAGCTGCCGGACCa < 1:127945/239‑1 (MQ=255)
c‑GGTGAAGGTTGT‑GGAAACAACCACGCCCG‑CCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAGTACATCGCTAAAGAAAT‑GCCCACGGCACC‑AAAGATTTTTGAGTTACCGTGC‑AGGG‑C‑AAAACCGCCTTCCGGGAACAACGATTTCAGCGGCTCGGCGCTCAAACTGAACTCTTGCAGATGCTGCGCCCAGTACATCTGAATGCCGCCTTCAACAGCTGCCGGACCAAAGATaaa < 1:20137/238‑1 (MQ=255)
gggTAAAGGTTGG‑GGGAAACACAAAGCCCG‑CCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAGTACATCGCTAAAGAAAT‑GCCCACGGCACC‑AAAGATTGTTGAGTTACCGTGC‑AGGG‑C‑AAAACCGCCTTCCGGGAACAACGATTTCAGCGGCTCGGCGCTCAAACTGAACTCTTGCAGATGCTGCGCCCAGTACATCTGAATGCCGCCTTCAACAGCTGCCGGACCAAAGATaaa < 1:389163/237‑1 (MQ=255)
cgtttAGGGGTGC‑GAGACGCAACAACCCCG‑CCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAGTACATCGCTAAAGAAAT‑GCCCACGGCACC‑AAAGATTTTTGAGTTACCGTGC‑AGGG‑C‑AAAACCGCCTTCCGGGAACAACGATTTCAGCGGCTCGGCGCTCAAACTGAACTCTTGCAGATGCTGCGCCCAGTACATCTGAATGCCGCCTTCAACAGCTGCCGGACCAAAGATaaa < 1:57365/235‑1 (MQ=255)
attGC‑GGAAATCAGCACGCCCG‑CCA‑CTTTTACCCTATTTTCCGGTGCGGCAGTGAAGTACATCGCTAAAGAAAT‑GCCCACGGCACC‑AAAGATTTTTGAGTTACCGTGC‑AGGG‑C‑AAAACCGCCTTCCGGGAACAACGATTTCAGCGGCTCGGCGCTCAAACTGAACTCTTGCAGATGCTGCGCCCAGTACATCTGAATGCCGCCTTCAACAGCTGCCGGACCAAAGATAAACTGTCCGt < 1:102933/237‑1 (MQ=255)
|
TATCCGCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACCTAGTCAATCAGACCTCCGCCCATGTTGCCCACCACACCAAAGAGATACATTACGGTCGACATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAATTCCAGCGGTTCGGTAATTCCCACCAGCATGGC‑GGTTAAGGTTGC‑GGGAATCAGCAAGCCCG‑CCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAGTACATCGCTAAAGAAAT‑GCCCACGGCACC‑AAAGATTTTTGAGTTACCGTGC‑AGGG‑C‑AAAACCGCCTTCCGGGAACAACGATTTCAGCGGCTCGGCGCTCAAACTGAACTCTTGCAGATGCTGCGCCCAGTACATCTGAATGCCGCCTTCAACAGCTGCCGGACCAAAGATAAACTGTCCGT > NC_000913/3862451‑3862897
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
