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 |
1,122,270 |
(A)6→5 |
coding (9/924 nt) |
yceM → |
Gfo/Idh/MocA family oxidoreductase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,122,265 | 0 | A | . | 96.5%
| 111.6
/ ‑1.2
| 29 | coding (4/924 nt) | yceM | Gfo/Idh/MocA family oxidoreductase |
| Reads supporting (aligned to +/- strand): ref base A (0/0); major base . (10/18); minor base G (1/0); total (11/18) |
| Fisher's exact test for biased strand distribution p-value = 3.79e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.78e-01 |
GGCCCGCGTCGAAGCCCTGGAAATCGAAGTGGCAGAACTGAAACAGCGTCTTGATTCGTTGCTGGCCCATCTGGGAGATTAAAGTGAAAAAATTACGTATCGGCGTAGTGGGATTAGGTGGCATTGCGCAAAAAGCGTGGTTACCGGTGCTGGCGGCAGCGTCTGACTGGAC > NZ_CP009273/1122179‑1122350
|
ggCCCGCGTCGAAGCCCTGGAAATCGAAGTGGCAGAACTGAAACAGCGTCTTGATTCGTTGCTGGCCCATCTGGGAGATTAAAGTGaaaa > 1:1219347/1‑90 (MQ=255)
cccGCGTCGAAGCCCTGGAAATCGAAGTGGCAGAACTGAAACAGCGTCTTGATTCGTTGCTGGCCCATCTGGGAGATTAAAGTGaaaaat > 2:760530/1‑89 (MQ=255)
ccGCGTCGAAGCCCTGGAAATCGAAGTGGCAGAACTGAAACAGCGTCTTGATTCGTTGCTGGCCCATCTGGGAGATTAAAGTGaaaaatt < 2:557774/90‑3 (MQ=255)
gcgTCGAAGCCCTGGAAATCGAAGTGGCAGAACTGAAACAGCGTCTTGATTCGTTGCTGGCCCATCTGGGAGATTAAAGTGaaaaattac > 2:1028886/1‑86 (MQ=255)
gcgTCGAAGCCCTGGAAATCGAAGTGGCAGAACTGAAACAGCGTCTTGATTCGTTGCTGGCCCATCTGGGAGATTAAAGTGaaaaattac > 2:914872/1‑86 (MQ=255)
gcgTCGAAGCCCTGGAAATCGAAGTGGCAGAACTGAAACAGCGTCTTGATTCGTTGCTGGCCCATCTGGGAGATTAAAGTGaaaaattac > 2:1410695/1‑86 (MQ=255)
gTCGAAGCCCTGGAAATCGAAGTGGCAGAACTGAAACAGCGTCTTGATTCGTTGCTGGCCCATCTGGGAGATTAAAGTG‑AAAAATTACGt < 1:1230938/90‑1 (MQ=255)
gCCCTGGAAATCGAAGTGGCAGAACTGAAACAGCGTCTTGATTCGTTGCTGGCCCATCTGGGAGATTAAAGTG‑AAAAATTACGTATCGGc < 2:1219347/90‑1 (MQ=255)
cTGGAAATCGAAGTGGCAGAACTGAAACAGCGTCTTGATTCGTTGCTGGCCCATCTGGGAGATTAAAGTG‑AAAAATTACGTATCGGCGTa < 1:152580/90‑1 (MQ=255)
tCGAAGTGGCAGAACTGAAACAGCGTCTTGATTCGTTGCTGGCCCATCTGGGAGATTAAAGTG‑AAAAATTACGTATCGGCGTAGTGGGAt < 1:168235/90‑1 (MQ=255)
tCGAAGTGGCAGAACTGAAACAGCGTCTTGATTCGTTGCTGGCCCATCTGGGAGATTAAAGTG‑AAAAATTACGTATCGGCGTAGTGGGAt < 2:724320/90‑1 (MQ=255)
tCGAAGTGGCAGAACTGAAACAGCGTCTTGATTCGTTGCTGGCCCATCTGGGAGATTAAAGTG‑AAAAATTACGTATCGGCGTAGTGGGAt < 2:933975/90‑1 (MQ=255)
gAAACAGCGTCTTGATTCGTTGCTGGCCCATCTGGGAGATTAAAGTG‑AAAAATTACGTATCGGCGTAGTGGGATTAGGTGGCATTGCGCa > 2:1254613/1‑90 (MQ=255)
aaCAGCGTCTTGATTCGTTGCTGGCCCATCTGGGAGATTAAAGTG‑AAAAATTACGTATCGGCGTAGTGGGATTAGGTGGCATTGCGCaaa > 1:145868/1‑90 (MQ=255)
gCGTCTTGATTCGTTGCTGGCCCATCTGGGAGATTAAAGTG‑AAAAATTACGTATCGGCGTAGTGGGATTAGGTGGCATTGCGCAAAAAGc > 2:1415479/1‑90 (MQ=255)
gCGTCTTGATTCGTTGCTGGCCCATCTGGGAGATTAAAGTG‑AAAAATTACGTATCGGCGTAGTGGGATTAGGTGGCATTGCGCAAAAAGc > 1:892268/1‑90 (MQ=255)
cGTCTTGATTCGTTGCTGGCCCATCTGGGAGATTAAAGTG‑AAAAATTACGTATCGGCGTAGTGGGATTAGGTGGCATTGCGCAAAAAGCg < 1:104683/90‑1 (MQ=255)
ttGATTCGTTGCTGGCCCATCTGGGAGATTAAAGTG‑AAAAATTACGTATCGGCGTAGTGGGATTAGGTGGCATTGCGCAAAAAGCGTGGt > 2:952460/1‑90 (MQ=255)
ttCGTTGCTGGCCCATCTGGGAGATTAAAGTG‑AAAAATTACGTATCGGCGTAGTGGGATTAGGTGGCATTGCGCAAAAAGCGTGGTTAcc < 1:182449/90‑1 (MQ=255)
ttCGTTGCTGGCCCATCTGGGAGATTAAAGTG‑AAAAATTACGTATCGGCGTAGTGGGATTAGGTGGCATTGCGCAAAAAGCGTGGTTAcc < 1:1028886/90‑1 (MQ=255)
ttCGTTGCTGGCCCATCTGGGAGATTAAAGTG‑AAAAATTACGTATCGGCGTAGTGGGATTAGGTGGCATTGCGCAAAAAGCGTGGTTAcc < 1:1410695/90‑1 (MQ=255)
ttCGTTGCTGGCCCATCTGGGAGATTAAAGTG‑AAAAATTACGTATCGGCGTAGTGGGATTAGGTGGCATTGCGCAAAAAGCGTGGTTAcc < 2:1471630/90‑1 (MQ=255)
ttCGTTGCTGGCCCATCTGGGAGATTAAAGTG‑AAAAATTACGTATCGGCGTAGTGGGATTAGGTGGCATTGCGCAAAAAGCGTGGTTAcc < 2:145868/90‑1 (MQ=255)
ttCGTTGCTGGCCCATCTGGGAGATTAAAGTG‑AAAAATTACGTATCGGCGTAGTGGGATTAGGTGGCATTGCGCAAAAAGCGTGGTTAcc < 1:861434/90‑1 (MQ=255)
ttCGTTGCTGGCCCATCTGGGAGATTAAAGTG‑AAAAATTACGTATCGGCGTAGTGGGATTAGGTGGCATTGCGCAAAAAGCGTGGTCAcc < 1:341321/90‑1 (MQ=255)
tGCTGGCCCATCTGGGAGATTAAAGTG‑AAAAATTACGTATCGGCGTAGTGGGATTAGGTGGCATTGCGCAAAAAGCGTGGTTACCGGTGc > 1:937825/1‑90 (MQ=255)
aTCTGGGAGATTAAAG‑GGAAAAATTACGTATCGGCGTAGTGGGATTAGGTGGCATTGCGCAAAAAGCGGGGTTACCGGTGCTGGCGGCAg > 1:1393920/1‑90 (MQ=255)
gaTTAAAGTG‑CAAAATTACGTATCGGCGTAGTGGGATTAGGTGGCATTGCGCAAAAAGCGTGGTTACCGGTGCTGGCGGCAGCGTCTGAc < 1:1518565/90‑1 (MQ=255)
ttAAAGTG‑AAAAATTACGTATCGGCGTAGTGGGATTAGGTGGCATTGCGCAAAAAGCGTGGTTACCGGTGCTGGCGGCAGCGTCTGACTg > 2:672924/1‑90 (MQ=255)
ttAAAGTG‑AAAAATTACGTATCGGCGTAGTGGGATTAGGTGGCATTGCGCAAAAAGCGTGGTTACCGGTGCTGGCGGCAGCGTCTGACTg > 2:1234223/1‑90 (MQ=255)
ttAAAGTG‑AAAAATTACGTATCGGCGTAGTGGGATTAGGTGGCATTGCGCAAAAAGCGTGGTTACCGGTGCTGGCGGCAGCGTCTGACTg > 2:886172/1‑90 (MQ=255)
aaaGTG‑AAAAATTACGTATTGGCGTAGTGGGATTAGGTGGCATTGCGCAAAAAGCGTGGTTACCGGTGCTGGCGGCAGCGTCTGACTGGa < 1:914872/90‑1 (MQ=255)
aaaGTG‑AAAAATTACGTATCGGCGTAGTGGGATTAGGTGGCATTGCGCAAAAAGCGTGGTTACCGGTGCTGGCGGCAGCGTCTGACTGGa < 1:952460/90‑1 (MQ=255)
aaaGTG‑AAAAATTACGTACCGGCGTAGTGGGATTAGGTGGCATTGCGCTAAAAGCGGGGTTATTGGTGCTGGCGGCAGCGTCTGACGGGa < 1:1345517/90‑1 (MQ=255)
aaGTG‑AAAAATTACGTATCGGCGTAGTGGGATTAGGTGGCATTGCGCAAAAAGCGTGGTTACCGGTGCTGGCGGCAGCGTCTGACTGGAc > 2:648208/1‑90 (MQ=255)
|
GGCCCGCGTCGAAGCCCTGGAAATCGAAGTGGCAGAACTGAAACAGCGTCTTGATTCGTTGCTGGCCCATCTGGGAGATTAAAGTGAAAAAATTACGTATCGGCGTAGTGGGATTAGGTGGCATTGCGCAAAAAGCGTGGTTACCGGTGCTGGCGGCAGCGTCTGACTGGAC > NZ_CP009273/1122179‑1122350
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 31 ≤ 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
GATTTACAGGCCCGCGTCGAAGCCCTGGAAATCGAAGTGGCAGAACTGAAACAGCGTCTTGATTCGTTGCTGGCCCATCTGGGAGATTAAAGTGAAAAAATTACGTATCGGCGTAGTGGGATTAGGTGGCATTGCGCAAAAAGCGTGGTTACCGGTGCTGGCGGCAGCGTCTGACTGGACGTTACAAGGAG > NZ_CP009273/1122171‑1122361
|
GATTTACAGGCCCGCGTCGAAGCCCTGGAAATCGAAGTGGCAGAACTGAAACAGCGTCTTGATTCGTTGCTGGCCCATCTGGGAGATTAAAGTGAAAAAT < SRR3722078.19061/100‑1 (MQ=60)
GATTTACAGGCCCGCGCGGAAGCCCTGGAAAACGAAGTGGAAGAACTGAAAAAGCGTCTTTATTCGTTGCTGGCCCATCTGGGAGATTAAAGTGAAAAAT < SRR3722078.1200044/100‑1 (MQ=60)
GTCGAAGCCCTGGAAATCGAAGTGGCAGAACTGAAACAGCGTCTTGATTCGTTGCTGGCCCATCTGGGAGATTAAAGTG‑AAAAATTACGTATCGGCGTAG < SRR3722078.1250338/100‑1 (MQ=60)
CTGGAAATCGAAGTGGCAGAACTGAAACAGCGTCTTGATTCGTTGCTGGCCCATCTGGGAGATTAAAGTG‑AAAAATTACGTATCGGCGTAGTGGGATTAG < SRR3722078.154348/100‑1 (MQ=60)
TCGAAGTGGCAGAACTGAAACAGCGTCTTGATTCGTTGCTGGCCCATCTGGGAGATTAAAGTG‑AAAAATTACGTATCGGCGTAGTGGGATTAGGTGGCAT < SRR3722078.170185/100‑1 (MQ=60)
GCAGAACTGAAACAGCGTCTTGATTCGTTGCTGGCCCATCTGGGAGATTAAAGTG‑AAAAATTACGTATCGGCGTAGTGGGATTAGGTGGCATTGCGCAAA > SRR3722078.147562/1‑100 (MQ=60)
AACTGAAACAGCGTCTTGATTCGTTGCTGGCCCATCTGGGAGATTAAAGTG‑AAAAATTACGTATCGGCGTAGTGGGATTAGGTGGCATTGCGCAAAAAGC > SRR3722078.904263/1‑100 (MQ=60)
CGTCTTGATTCGTTGCTGGCCCATCTGGGAGATTAAAGTG‑AAAAATTACGTATCGGCGTAGTGGGATTAGGTGGCATTGCGCAAAAAGCGTGGTTACCGG < SRR3722078.105926/100‑1 (MQ=60)
CTTGATTCGTTGCTGGCCCATCTGGGAGATTAAAGTG‑AAAAATTACGTATCGGCGTAGTGGGATTAGGTGGCATTGCGCAAAAAGCGTGGTTACCGGTGC > SRR3722078.950831/1‑100 (MQ=60)
TTCGTTGCTGGCCCATCTGGGAGATTAAAGTG‑AAAAATTACGTATCGGCGTAGTGGGATTAGGTGGCATTGCGCAAAAAGCGTGGTTACCGGTGCTGGCG < SRR3722078.1433586/100‑1 (MQ=60)
TTCGTTGCTGGCCCATCTGGGAGATTAAAGTG‑AAAAATTACGTATCGGCGTAGTGGGATTAGGTGGCATTGCGCAAAAAGCGTGGTTACCGGTGCTGGCG < SRR3722078.184612/100‑1 (MQ=60)
TTCGTTGCTGGCCCATCTGGGAGATTAAAGTG‑AAAAATTACGTATCGGCGTAGTGGGATTAGGTGGCATTGCGCAAAAAGCGTGGTTACCGGTGCTGGCG < SRR3722078.872958/100‑1 (MQ=60)
TTCGTTGCTGGCCCATCTGGGAGATTAAAGTG‑AAAAATTACGTATCGGCGTAGTGGGATTAGGTGGCATTGCGCAAAAAGCGTGGTTACCGGTGCTGGCG < SRR3722078.1044158/100‑1 (MQ=60)
TTCGTTGCTGGCCCATCTGGGAGATTAAAGTG‑AAAAATTACGTATCGGCGTAGTGGGATTAGGTGGCATTGCGCAAAAAGCGTGGTCACCGGTGCTGGCG < SRR3722078.345498/100‑1 (MQ=60)
TTGCTGGCCCATCTGGGAGATTAAAG‑GGAAAAATTACGTATCGGCGTAGTGGGATTAGGTGGCATTGCGCAAAAAGCGGGGTTACCGGTGCTGGCGGCAG > SRR3722078.1416446/1‑100 (MQ=60)
GATTAAAGTG‑CAAAATTACGTATCGGCGTAGTGGGATTAGGTGGCATTGCGCAAAAAGCGTGGTTACCGGTGCTGGCGGCAGCGTCTGACTGGACGTTAC < SRR3722078.1543331/100‑1 (MQ=60)
AAAGTG‑AAAAATTACGTATTGGCGTAGTGGGATTAGGTGGCATTGCGCAAAAAGCGTGGTTACCGGTGCTGGCGGCAGCGTCTGACTGGACGTTACAAGG < SRR3722078.927289/100‑1 (MQ=60)
AAAGTG‑AAAAATTACGTATCGGCGTAGTGGGATTAGGTGGCATTGCGCAAAAAGCGTGGTTACCGGTGCTGGCGGCAGCGTCTGACTGGACGTTACAAGG < SRR3722078.965854/100‑1 (MQ=60)
AAAGTG‑AAAAATTACGTACCGGCGTAGTGGGATTAGGTGGCATTGCGCTAAAAGCGGGGTTATTGGTGCTGGCGGCAGCGTCTGACGGGACGTTCCAAGG < SRR3722078.1367113/100‑1 (MQ=60)
AGTG‑AAAAATTACGTATCGGCGTAGTGGGATTAGGTGGCATTGCGCAAAAAGCGTGGTTACCGGTGCTGGCGGCAGCGTCTGACTGGACGTTACAAGGAG < SRR3722078.1343518/100‑1 (MQ=60)
|
GATTTACAGGCCCGCGTCGAAGCCCTGGAAATCGAAGTGGCAGAACTGAAACAGCGTCTTGATTCGTTGCTGGCCCATCTGGGAGATTAAAGTGAAAAAATTACGTATCGGCGTAGTGGGATTAGGTGGCATTGCGCAAAAAGCGTGGTTACCGGTGCTGGCGGCAGCGTCTGACTGGACGTTACAAGGAG > NZ_CP009273/1122171‑1122361
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
