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 |
|
A12 F1 I1 R1
|
760 |
58.2 |
3022526 |
90.8% |
2744453 |
102.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
3,728,118 |
(C)8→9 |
coding (1254/1455 nt) |
xylB ← |
xylulokinase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 3,728,110 | 1 | . | C | 85.2%
| 79.5
/ 7.3
| 27 | coding (1262/1455 nt) | xylB | xylulokinase |
| Reads supporting (aligned to +/- strand): ref base . (1/3); new base C (10/13); total (11/16) |
| Fisher's exact test for biased strand distribution p-value = 6.24e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.87e-01 |
CTGATAAGCGGCATAACGCTGCGCATCTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGG‑‑CC‑CCACA‑‑T‑‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTAACACTTTGCGGTTTAATACCGCAGGCATG > NC_000913/3727974‑3728231
|
cTGATAAGCGGCATAACGCTGCGCATCTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGG‑‑CC‑CCACA‑‑T‑‑cc < 2:1243731/139‑1 (MQ=255)
aTAAGCGGCATAACGCTGCGCATCTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGG‑‑CC‑CCACA‑‑T‑‑ccccc < 1:740733/139‑1 (MQ=255)
aaCGCTGCGCATCTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGG‑‑CC‑CCACA‑‑TC‑CCCCCCCCGTACGGt < 2:456961/139‑1 (MQ=255)
cgcATCTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGG‑‑CC‑CCACA‑‑T‑‑cccccccccg < 2:658647/126‑3 (MQ=255)
cgcATCTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGG‑‑CC‑CCACA‑‑T‑‑cccccccccg > 1:658647/1‑124 (MQ=255)
tGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGG‑‑CC‑CCACA‑‑TCCCCCCCCCCGTACGGTAATCGAgctgct < 2:423895/139‑1 (MQ=255)
cGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGG‑‑CC‑CCACA‑‑T‑‑ccccccccccg > 2:1266536/1‑109 (MQ=255)
cGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGG‑‑CC‑CCACA‑‑T‑‑ccccccccccg < 1:1266536/112‑4 (MQ=255)
aCGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGG‑‑CC‑CCACA‑‑T‑‑ccccc < 2:27578/95‑1 (MQ=255)
aCGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGG‑‑CC‑CCACA‑‑T‑‑ccccc > 1:27578/1‑95 (MQ=255)
aaGTTCCGGAAACAATTAATTGGGCGTTTTTCCTGGTTTCCCCCCGTCCGCCGCCGGCCTTGCTG‑GCCCCGTGGTGGGCCCACCACC‑‑C‑‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCt < 2:557075/138‑1 (MQ=255)
aGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGG‑‑CC‑CCACA‑‑TCCCCCCCCCCGTACGGTAATCGAgctgct < 1:384994/114‑1 (MQ=255)
aGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGG‑‑CC‑CCACA‑‑TCCCCCCCCCCGTACGGTAATCGAgctgct > 2:384994/1‑114 (MQ=255)
ttGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGG‑‑CC‑CCACA‑‑TC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACg > 1:215220/1‑139 (MQ=255)
gCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGG‑‑CC‑CCACA‑‑TCCCCCCCCCCGTACGGTAATCGAGCTGCTGa < 2:805880/109‑1 (MQ=255)
gCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGG‑‑CC‑CCACA‑‑TCCCCCCCCCCGTACGGTAATCGAGCTGCTGa > 1:805880/1‑109 (MQ=255)
aacaaTTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGG‑‑CC‑CCACA‑‑TC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTAc < 2:215220/139‑1 (MQ=255)
aacaaTTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGG‑‑CC‑CCACA‑‑T‑‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATcc < 1:1403529/117‑1 (MQ=255)
aacaaTTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGG‑‑CC‑CCACA‑‑T‑‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATcc > 2:1403529/1‑117 (MQ=255)
acaaTTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGG‑‑CC‑CCACA‑‑TCCCCCCCCCCCTACCGAAATCGAGCTGCTGACCGCTGCTATCCGCCACCCTCTGCCCCCAGTAc > 1:855265/1‑139 (MQ=255)
caaTTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGG‑‑CC‑CCACA‑‑TCCCCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACt < 1:214807/139‑1 (MQ=255)
caaTTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGG‑‑CC‑CCACA‑‑T‑‑ccccccccccgta > 2:1206443/1‑82 (MQ=255)
caaTTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGG‑‑CC‑CCACA‑‑T‑‑ccccccccccgta < 1:1206443/87‑6 (MQ=255)
tGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGG‑‑CC‑CCACA‑‑T‑‑ccccccccccgtac > 1:1196363/1‑74 (MQ=255)
tGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGG‑‑CC‑CCACA‑‑T‑‑ccccccccccgtac < 2:1196363/80‑7 (MQ=255)
gCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGG‑‑CC‑CCACA‑‑TCCCCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGc < 2:1462369/121‑1 (MQ=255)
gCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGG‑‑CC‑CCACA‑‑TCCCCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGc > 1:1462369/1‑121 (MQ=255)
cgccgcGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGG‑‑CC‑CCACACCC‑‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACg < 2:1328040/139‑1 (MQ=255)
gccgcGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGG‑‑CC‑CCACA‑‑TCCCCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGatat < 2:1014889/87‑1 (MQ=255)
gccgcGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGG‑‑CC‑CCACA‑‑TCCCCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGatat > 1:1014889/1‑87 (MQ=255)
gccgcGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGG‑‑CC‑CCACA‑‑TCCCCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACg < 1:575028/103‑1 (MQ=255)
gccgcGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGG‑‑CC‑CCACA‑‑TCCCCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACg > 2:575028/1‑103 (MQ=255)
gccgcGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGG‑‑CC‑CCACA‑‑TC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTa > 1:1498751/1‑139 (MQ=255)
tGCGCCAGCCTTGCTGCGCCCAGTGCTGG‑‑CC‑CCACA‑‑TCCCCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTAACACTTTg < 2:133883/139‑1 (MQ=255)
ccAGTGCTGG‑‑CC‑CCACA‑‑TCCCCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTAACACTTTGCGGTTTAATACCGCAGGCa < 1:690621/139‑1 (MQ=255)
cAGTGCTGG‑‑CC‑CCACA‑‑TCCCCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTAACACTTTGCGGTTTAATACCGCAGGCAt < 2:855265/139‑1 (MQ=255)
aGTGCTGG‑‑CC‑CCACA‑‑TCCCCCCCCCCGTACGGTAATCGAg < 1:506294/40‑1 (MQ=255)
aGTGCTGG‑‑CC‑CCACA‑‑TCCCCCCCCCCGTACGGTAATCGAg > 2:506294/1‑40 (MQ=255)
aGTGCTGG‑‑CC‑CCACA‑‑TCCCCCCCCCCCCACGGCAATCGAAATGTTGAACGCTTATAACCCCCCGCCTCCGACGCCAGTACTCAAAACCCCGCCCGCCCCCAAACCACGTAACACATTGCCGCTTAATAACGcctgcacg > 2:1295201/1‑132 (MQ=255)
|
CTGATAAGCGGCATAACGCTGCGCATCTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGG‑‑CC‑CCACA‑‑T‑‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTAACACTTTGCGGTTTAATACCGCAGGCATG > NC_000913/3727974‑3728231
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
