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 F5 I102 R1
|
278 |
39.1 |
2251254 |
95.8% |
2156701 |
87.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
634,477 |
A→G |
E26G (GAA→GGA) |
ahpC → |
alkyl hydroperoxide reductase subunit C |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 634,477 | 0 | A | G | 100.0%
| 127.1
/ NA
| 35 | E26G (GAA→GGA) | ahpC | alkyl hydroperoxide reductase subunit C |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (18/17); total (18/17) |
GAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGAAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGT > NZ_CP009273/634389‑634561
|
gaggaAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGgaa < 1:618315/91‑1 (MQ=255)
aGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGa < 1:581745/91‑1 (MQ=255)
aGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGa > 2:39905/1‑91 (MQ=255)
aTGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAg > 2:647607/1‑91 (MQ=255)
aTGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAg < 2:35308/91‑1 (MQ=255)
tGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAgg > 2:821415/1‑91 (MQ=255)
gTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGc < 1:418361/91‑1 (MQ=255)
gTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGc > 2:328148/1‑91 (MQ=255)
ccTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCg > 2:808329/1‑91 (MQ=255)
ccTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCg > 1:53823/1‑91 (MQ=255)
ccTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCg > 1:826455/1‑91 (MQ=255)
tGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTg > 1:97319/1‑91 (MQ=255)
ttAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAg < 1:1061715/91‑1 (MQ=255)
ttAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAg < 2:209288/91‑1 (MQ=255)
aaCACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCg > 2:87034/1‑91 (MQ=255)
acacCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGt < 2:390833/91‑1 (MQ=255)
acacCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGt > 1:635877/1‑91 (MQ=255)
cacCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGtc > 1:426064/1‑91 (MQ=255)
ttttAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCg > 2:676764/1‑91 (MQ=255)
ttttAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCg > 2:1097329/1‑91 (MQ=255)
ttttAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCg > 1:315893/1‑91 (MQ=255)
ttAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGc < 2:629105/91‑1 (MQ=255)
aaaaaCCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTg < 2:1112068/91‑1 (MQ=255)
aaaaaCCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTg < 1:958311/91‑1 (MQ=255)
aaaaaCCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTg < 1:761727/91‑1 (MQ=255)
aCCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGactt < 1:244278/91‑1 (MQ=255)
aGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGactttac > 1:587956/1‑91 (MQ=255)
aaaCGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGc < 1:676764/91‑1 (MQ=255)
gCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCccgac < 2:842937/91‑1 (MQ=255)
gCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCccgac > 2:1112857/1‑91 (MQ=255)
gCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCccgac > 2:179984/1‑91 (MQ=255)
aTCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAAc < 1:877622/88‑1 (MQ=255)
aTCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAAc > 2:877622/1‑88 (MQ=255)
cGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGt < 2:893954/91‑1 (MQ=255)
aaTCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGAc < 2:635877/91‑1 (MQ=255)
tCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGt < 2:185918/91‑1 (MQ=255)
|
GAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGAAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGT > NZ_CP009273/634389‑634561
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ 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
TCGAAAACACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGAAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTACGA > NZ_CP009273/634378‑634576
|
TCGAAAACACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGA > SRR3722125.861484/1‑101 (MQ=60)
caagcagaagacggcatacgagatcatgcctagtctcgtgggctcggagatgtgtataagagacagTTCAAAAACGGCGAATTCATCGAAATCACCGGAAA < SRR3722125.123584/35‑1 (MQ=60)
GAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGA < SRR3722125.631646/101‑1 (MQ=60)
GTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCG > SRR3722125.844600/1‑101 (MQ=60)
GTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCG > SRR3722125.54814/1‑101 (MQ=60)
TAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTG > SRR3722125.99153/1‑101 (MQ=60)
AGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGG < SRR3722125.594234/101‑1 (MQ=60)
GTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCG < SRR3722125.427205/101‑1 (MQ=60)
TCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGT > SRR3722125.649579/1‑101 (MQ=60)
CCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTC > SRR3722125.435050/1‑101 (MQ=60)
TTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTC < SRR3722125.1085614/101‑1 (MQ=60)
AAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCG > SRR3722125.322383/1‑101 (MQ=60)
TTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTAC > SRR3722125.600580/1‑101 (MQ=60)
AAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTT < SRR3722125.778227/101‑1 (MQ=60)
AAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTT < SRR3722125.979653/101‑1 (MQ=60)
AAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGActgtctcttatacacatctccgagcccacgagactaggcatgatctc > SRR3722125.616005/1‑54 (MQ=60)
ACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTA < SRR3722125.249182/101‑1 (MQ=60)
AAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAAC < SRR3722125.691346/101‑1 (MQ=60)
TTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGT < SRR3722125.897032/101‑1 (MQ=60)
GGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTACGA < SRR3722125.15149/101‑1 (MQ=60)
|
TCGAAAACACGGAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGAAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTACGA > NZ_CP009273/634378‑634576
|
| 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: ‑ |
