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 F3 I96 R1
|
172 |
34.7 |
2005794 |
96.2% |
1929573 |
85.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,629,389 |
(T)8→7 |
intergenic (+42/+18) |
creD → / ← arcA |
cell envelope integrity protein CreD/two‑component system response regulator ArcA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,629,382 | 0 | T | . | 96.4%
| 107.3
/ ‑2.3
| 28 | intergenic (+35/+25) | creD/arcA | cell envelope integrity protein CreD/two‑component system response regulator ArcA |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base . (15/12); total (15/13) |
| Fisher's exact test for biased strand distribution p-value = 4.64e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TGAAAGCCAGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCGTTTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGCGATGATTTC > NZ_CP009273/4629295‑4629466
|
tGAAAGCCAGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCGttt > 1:939070/1‑90 (MQ=255)
aaaGCCAGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCGttttt > 1:816309/1‑90 (MQ=255)
cAGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCC‑TTTTTTTTGAc < 1:883892/90‑1 (MQ=255)
aGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCGtttttttgacg < 1:320614/90‑5 (MQ=255)
aGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCGtttttttgacg < 1:909751/90‑5 (MQ=255)
aGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCGtttttttgacg < 1:55177/90‑5 (MQ=255)
aGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCGtttttttgacg < 1:564638/90‑5 (MQ=255)
aGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCGtttttttgacg < 2:116233/90‑5 (MQ=255)
aagTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTaa < 2:145109/90‑1 (MQ=255)
agTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTaaa < 1:265372/90‑1 (MQ=255)
agTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTaaa > 2:591034/1‑90 (MQ=255)
gTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAg < 1:86661/90‑1 (MQ=255)
gACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAAt < 2:20714/90‑1 (MQ=255)
gACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAAt < 2:469725/90‑1 (MQ=255)
cGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCt < 2:751059/90‑1 (MQ=255)
aTGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTc > 1:720074/1‑90 (MQ=255)
tACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATc > 2:540183/1‑90 (MQ=255)
aCGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACAGTGGTAAAGCCGATTAATCTTCCAGATCa > 2:102309/1‑90 (MQ=255)
aTCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGc < 2:552953/90‑1 (MQ=255)
tGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGa > 2:102448/1‑90 (MQ=255)
tGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGa < 2:527827/90‑1 (MQ=255)
tGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGa > 1:846808/1‑90 (MQ=255)
tGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGa > 1:658795/1‑90 (MQ=255)
tAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGAt > 1:247837/1‑90 (MQ=255)
aGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATaa > 1:903117/1‑90 (MQ=255)
tGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACgg > 2:491/1‑43 (MQ=38)
tGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACgg < 1:491/43‑1 (MQ=38)
tGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGGTAACCtt > 1:952457/1‑90 (MQ=255)
tGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCtt > 1:785893/1‑90 (MQ=255)
tGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCtt > 2:656521/1‑90 (MQ=255)
aaaaCGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGaa < 1:495749/90‑1 (MQ=255)
aaaCGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAAt < 1:70150/90‑1 (MQ=255)
aaaaaGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGCgatg < 2:799088/90‑1 (MQ=255)
gcgcCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGCGATGATTtc > 1:151291/1‑90 (MQ=255)
gcgcCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGCGATGATTtc > 1:308190/1‑90 (MQ=255)
|
TGAAAGCCAGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCGTTTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGCGATGATTTC > NZ_CP009273/4629295‑4629466
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ 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
CAGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCGTTTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGCGATGATTTCCGGCGTATCCGGCGTAGAT > NZ_CP009273/4629302‑4629485
|
CAGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCC‑TTTTTTTTGACGGTGGTAAAG < SRR3722236.899439/100‑1 (MQ=60)
AGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGC < SRR3722236.925814/100‑1 (MQ=60)
AGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGC < SRR3722236.325202/100‑1 (MQ=60)
AGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGC < SRR3722236.55953/100‑1 (MQ=60)
AGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGC < SRR3722236.573329/100‑1 (MQ=60)
gccttcgtcggcagcgtcagatgtgtataagagacaGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCC < SRR3722236.501/64‑1 (MQ=60)
AGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAAT < SRR3722236.269254/100‑1 (MQ=60)
GTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATC < SRR3722236.87861/100‑1 (MQ=60)
ACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTC > SRR3722236.732277/1‑100 (MQ=60)
GTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGA > SRR3722236.861635/1‑100 (MQ=60)
GTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGA > SRR3722236.669715/1‑100 (MQ=60)
TATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGAT > SRR3722236.251514/1‑100 (MQ=60)
TCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAA > SRR3722236.919045/1‑100 (MQ=60)
GAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGGTAACCTT > SRR3722236.969262/1‑100 (MQ=60)
GAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTT > SRR3722236.799480/1‑100 (MQ=60)
AAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGCGAT < SRR3722236.503229/100‑1 (MQ=60)
AAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGCGATG < SRR3722236.71141/100‑1 (MQ=60)
GCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGCGATGATTTC > SRR3722236.312626/1‑100 (MQ=60)
GCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGCGATGATTTC > SRR3722236.153497/1‑100 (MQ=60)
GCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGGGAATGGTGGCGATGATTTCCG > SRR3722236.770272/1‑100 (MQ=60)
AAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGCGATGATTTCCGGCG > SRR3722236.284081/1‑100 (MQ=60)
GTTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGCGATGATTTCCGGCGTATCCGGCGT < SRR3722236.292226/100‑1 (MQ=60)
TTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCctgtctcttatacacatctgacgctgccgacgaaggcttaggtgtagatctcgggggtcgccgt > SRR3722236.570334/1‑36 (MQ=60)
|
CAGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCGTTTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGCGATGATTTCCGGCGTATCCGGCGTAGAT > NZ_CP009273/4629302‑4629485
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
