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 |
|
A13 F40 I1 R1
|
12 |
34.5 |
773110 |
93.2% |
720538 |
148.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
USA300TCH1516_ALE |
2,627,280 |
(AT)5→6 |
intergenic (‑218/‑107) |
sarT ← / → sarU |
HTH‑type transcriptional regulator SarT/HTH‑type transcriptional regulator SarU |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | USA300TCH1516_ALE | 2,627,269 | 1 | . | T | 94.4%
| 56.7
/ ‑2.2
| 18 | intergenic (‑207/‑118) | sarT/sarU | HTH‑type transcriptional regulator SarT/HTH‑type transcriptional regulator SarU |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base T (7/10); total (7/11) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.01e-01 |
| * | USA300TCH1516_ALE | 2,627,269 | 2 | . | A | 94.4%
| 58.1
/ ‑2.0
| 18 | intergenic (‑207/‑118) | sarT/sarU | HTH‑type transcriptional regulator SarT/HTH‑type transcriptional regulator SarU |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base A (7/10); total (7/11) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.43e-01 |
ATAACTCCAAATATATTTAGTTTGTGGTGCTAGCTATAAACACAAATGAATCATAACACTATATTTTGATTTTGTTCAATTGTTTTTATTTTTGGATAATAAATGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTT‑‑TATATATATATTATATATAAAATATTTAGGTTAACATGTCTTTAAAAGAGATTGCTTTTATATTACTTTAAATAATATAAAGTATTGGGACATCAGAAAATAGTAGGAGAATGTAAGGTGGACTATCAAACTTTCGAAAAG > USA300TCH1516_ALE/2627122‑2627410
||
ataaCTCCAAATATATTTAGTTTGTGGTGCTAGCTATAAACACAAATGAATCATAACACTATATTTTGATTTTGTTCAATGGTTTTTATTTTTGGATAATAAATGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTAtttatattt > 1:233087/1‑148 (MQ=255)
cAAATATATTTAGTTTGTGGTGCTAGCTATAAACACAAATGAATCATAACACTATATTTTGATTTTGTTCAATTGTTTTTATTTTTGGATAATAAATGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTT‑‑tatatat < 1:58478/148‑1 (MQ=255)
atatTTAGTTTGTGGTGCTAGCTATAAACACAAATGAATCATAACACTATATTTTGATTTTGTTCAATTGTTTTTATTTTTGGATAATAAATGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTT‑‑Tatatatatata < 2:361826/148‑2 (MQ=255)
tctagctaTAAACACATATGAATCATAACACTATATTTTGATTTTGTTCAATTGTTTTTATTTTTGGATAATAAATGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTTTATATATATATATTATATATAAAATAtt < 2:318717/147‑1 (MQ=255)
gctaTAAACACAAATGAATCATAACACTATATTTTGATTTTGTTCAATTGTTTTTATTTTTGGATAATAAATGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTTTATATATATATATTATATATAAAATATTTAgg > 1:125275/1‑148 (MQ=255)
gctaTAAACACAAATGAATCATAACACTATATTTTGATTTTGTTCAATTGTTTTTATTTTTGGATAATAAATGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTTTATATATATATATTATATATAAAATATTTAgg < 2:123757/148‑1 (MQ=255)
gctaTAAACACAAATGAATCATAACACTATATTTTGATTTTGTTCAATTGTTTTTATTTTTGGATAATAAATGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTTTATATATATATATTATATATAAAATATTTAgg > 1:354458/1‑148 (MQ=255)
ctaTAAACACAAATGAATCATAACACTATATTTTGATTTTGTTCAATTGTTTTTATTTTTGGATAATAAATGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTTTATATATATATATTATATATAAAATATTTAGGt > 1:172055/1‑148 (MQ=255)
aaTGAATCATAACACTATATTTTGATTTTGTTCAATTGTTTTTATTTTTGGATAATAAATGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTTTATATATATATATTATATATAAAATATTTAGGTTAACATGTCtt < 1:152978/148‑1 (MQ=255)
aaTGAATCATAACACTATATTTTGATTTTGTTCAATTGTTTTTATTTTTGGATAATAAATGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTTTATATATATATATTATATATAAAATATTTAGGTTAACATGTCtt > 1:306936/1‑148 (MQ=255)
aTGAATCATAACACTATATTTTGATTTTGTTCAATTGTTTTTATTTTTGGATAATAAATGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTTTATATATATATATTATATATAAAATATTTAGGTTAACATGTCttt > 2:354769/1‑148 (MQ=255)
tGTTTTTATTTTTGGATAATAAATGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTTTATATATATATATTATATATAAAATATTTATGTTAACATGTCTTTAAAAGAGATTGCTTTTATATTACTTTTaatatttt > 2:384513/1‑144 (MQ=255)
gATAATAAATGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTTTATATATATATATTATATATAAAATATTTAGGTTAACATGTCTTTAAAAGAGATTGCTTTTATATTACTTTAAATAATATAAAGTATTGGGACa < 1:87222/148‑1 (MQ=255)
aTGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTTTATATATATATATTATATATAAAATATTTAGGTTAACATGTCTTTAAAAGAGATTGCTTTTATATTACTTTAAATAATATAAAGTATTGGGACATCAGaaaa < 2:172055/148‑1 (MQ=255)
aaTTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTTTATATATATATATTATATATAAAATATTTAGGTTAACATGTCTTTAAAAGAGATTGCTTTTATATTACTTTAAATAATATAAAGTATTGGGACATCAGAAAAtag < 1:361464/148‑1 (MQ=255)
aaTTTGTCATTTGTTATTATGTGATTTTTAGTTATTTATATTTTATATATATATATTCTATATAAAATATTTAGGTTAACATGTCTTTAAAAGAGATTGCTTTTATATTACTTTAAATAATATAAAGTATTGGGACATCAGAAAAtag < 1:202123/148‑1 (MQ=255)
tATTCTGTGATTTTTAGTTATTTATATTTTATATATATATATTATATATAAAATATTTAGGTTAACATGTCTTTAAAAGAGATTGCTTTTATATTACTTTAAATAATATAAAGTATTGGGACATCAGAAAATAGTAGGAGAATGTAAg > 1:13908/1‑148 (MQ=255)
ttAGTTATTTATATTTTATATATATATATTATATATAAAATATTTAGGTTAACATGTCTTTAAAAGAGATTGCTTTTATATTACTTTAAATAATATAAAGTATTGGGACATCAGAAAATAGTAGGAGAATGTAAGGTGGACTATCaaa < 1:338454/148‑1 (MQ=255)
ttAGTTATTTATATTTTATATATATATATTATATATAAAATATTTAGGTTAACATGTCTTTAAAAGAGATTGCTTTTATATTACTTTAAATAATATAAAGTATTGGGACATCAGAAAATAGTAGGAGAATGTAAGGTGGACTATCaaa < 1:108088/148‑1 (MQ=255)
ttatatttta‑‑tatatATATATTATATATAAAATATTTAGGTTAACATGTCTTTAAAAGAGATTGCTTTTATATTACTTTAAATAATATAAAGTATTGGGACATCAGAAAATAGTAGGAGAATGTAAGGTGGACTATCAAACTTTCGaa < 2:270985/145‑1 (MQ=255)
atttatATTTTATATATATATATTATATATAAAATATTTAGTTTAACATGTATTTAAAAGAGATTGCTTTTATATTACTTTAAATAATATAAAGTATTGGGACATCAGAAAATAGTAGGAGAATGTAAGGTGGACTATCAAACTTTCg < 2:22230/148‑1 (MQ=255)
tatttta‑‑tatatATATATTATATATAAAATATTTAGGTTAACATGTCTTTAAAAGAGATTGCTTTTATATTACTTTAAATAATATAAAGTATTGGGACATCAGAAAATAGTAGGAGAATGTAAGGTGGACTATCAAACTTTCGAAAAg < 1:23152/148‑1 (MQ=255)
||
ATAACTCCAAATATATTTAGTTTGTGGTGCTAGCTATAAACACAAATGAATCATAACACTATATTTTGATTTTGTTCAATTGTTTTTATTTTTGGATAATAAATGAATTTGTCATTTGTTATTCTGTGATTTTTAGTTATTTATATTT‑‑TATATATATATTATATATAAAATATTTAGGTTAACATGTCTTTAAAAGAGATTGCTTTTATATTACTTTAAATAATATAAAGTATTGGGACATCAGAAAATAGTAGGAGAATGTAAGGTGGACTATCAAACTTTCGAAAAG > USA300TCH1516_ALE/2627122‑2627410
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
