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 F4 I88 R1
|
217 |
30.5 |
1742422 |
95.9% |
1670982 |
87.3 |
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%
| 97.6
/ NA
| 27 | E26G (GAA→GGA) | ahpC | alkyl hydroperoxide reductase subunit C |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (15/12); total (15/12) |
AGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGAAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGAC > NZ_CP009273/634399‑634559
|
aGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGa > 1:397460/1‑91 (MQ=255)
aGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGa > 1:438539/1‑91 (MQ=255)
aGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGa < 2:397460/91‑1 (MQ=255)
aTGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAg < 2:438539/91‑1 (MQ=255)
aTGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAg < 2:214756/91‑1 (MQ=255)
tGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAgg > 2:457548/1‑91 (MQ=255)
gTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGc > 1:455857/1‑91 (MQ=255)
tCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGcc > 1:277576/1‑91 (MQ=255)
ccTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCg > 1:156453/1‑91 (MQ=255)
ccTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCg > 2:697913/1‑91 (MQ=255)
ccTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCg > 1:350734/1‑91 (MQ=255)
ccTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCg > 2:155394/1‑91 (MQ=255)
ttGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCt > 1:597505/1‑91 (MQ=255)
ttAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAg < 2:805426/91‑1 (MQ=255)
ttAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAg < 2:597505/91‑1 (MQ=255)
aaaaTTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGtcttct > 1:162751/1‑91 (MQ=255)
aaaCCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGtcttcttcttct > 2:335207/1‑91 (MQ=255)
tttAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCgg > 2:803186/1‑91 (MQ=255)
tttAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCgg > 1:31449/1‑91 (MQ=255)
aaaaaCCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTg < 1:573273/91‑1 (MQ=255)
aaaaaCCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTg < 2:496151/91‑1 (MQ=255)
aGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGactttac > 2:823271/1‑91 (MQ=255)
ggCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTGCCCGGCTGactttact < 2:156453/91‑1 (MQ=255)
ggCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGactttact < 1:481196/91‑1 (MQ=255)
aaaCGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGc < 1:457548/91‑1 (MQ=255)
gCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGTGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCccgac < 2:455857/91‑1 (MQ=255)
aaTCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGAc < 1:335207/91‑1 (MQ=255)
|
AGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGAAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGAC > NZ_CP009273/634399‑634559
|
| 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
GAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGAAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTACGA > NZ_CP009273/634389‑634576
|
GAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGA > SRR3722118.405795/1‑101 (MQ=60)
GAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGA > SRR3722118.447784/1‑101 (MQ=60)
AAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGC > SRR3722118.465457/1‑101 (MQ=60)
AGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCC > SRR3722118.283270/1‑101 (MQ=60)
GTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCG > SRR3722118.159483/1‑101 (MQ=60)
GTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCG > SRR3722118.358006/1‑101 (MQ=60)
ATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCT > SRR3722118.610222/1‑101 (MQ=60)
GATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCT > SRR3722118.165931/1‑101 (MQ=60)
AATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGG > SRR3722118.32019/1‑101 (MQ=60)
AAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACCTT < SRR3722118.585424/101‑1 (MQ=60)
GGCATTCAAAAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCC < SRR3722118.491382/101‑1 (MQ=60)
AAACGGCGAATTCATCGAAATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAAC < SRR3722118.467186/101‑1 (MQ=60)
AATCACCGGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACC < SRR3722118.342110/101‑1 (MQ=60)
GGAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTACGA < SRR3722118.226005/101‑1 (MQ=60)
|
GAGGAAGTATAGATGTCCTTGATTAACACCAAAATTAAACCTTTTAAAAACCAGGCATTCAAAAACGGCGAATTCATCGAAATCACCGAAAAAGATACCGAAGGCCGCTGGAGCGTCTTCTTCTTCTACCCGGCTGACTTTACTTTCGTATGCCCGACCGAACTGGGTGACGTTGCTGACCACTACGA > NZ_CP009273/634389‑634576
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ 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: ‑ |
