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 |
1,370,044 |
(T)9→8 |
intergenic (+41/‑172) |
pspE → / → ycjM |
thiosulfate:cyanide sulfurtransferase (rhodanese)/alpha amylase catalytic domain family protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 1,370,036 | 0 | T | . | 94.9%
| 137.8
/ 2.2
| 39 | intergenic (+33/‑180) | pspE/ycjM | thiosulfate:cyanide sulfurtransferase (rhodanese)/alpha amylase catalytic domain family protein |
| Reads supporting (aligned to +/- strand): ref base T (1/1); new base . (18/19); total (19/20) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.05e-01 |
AGTCAGGGCAAGCAAAAGAGATCCTTAGCGAGATGGGATATACCCACGTTGAGAACGCCGGTGGCCTGAAAGACATCGCAATGCCGAAGGTCAAAGGTTAAAAGAATTCACCATGAGCGGCGCTTATGCGCCGTTTTTTTTTCTGTCACACCTTATTTACAT‑CCCCATAGATTATTTGCGTCAGCTCACAAATACGCTTTTTCCCTGGTAAAAAATGATTTCCTGCGTGACTAAAACCCTTGTGCTCAATTGACAGTTTATTTTCTG > NC_000913/1369903‑1370169
|
aGTCAGGGCAAGCAAAAGAGATCCTTAGCGAGATGGGATATACCCACGTTGAGAACGCCGGTGGCCTGAAAGACATCGCAATGCCGAAGGTCAAAGGTTAAAAGAATTCACCATGAGCGGCGCTTATGCGCCGtttttt < 2:13994/139‑1 (MQ=255)
agcaaAAGAGATCCTTAGCGAGATGGGATATACCCACGTTGAGAACGCCGGTGGCCTGAAAGACATCGCAATGCCGAAGGTCAAAGGTTAAAAGAATTCACCATGAGCGGCGCTTATGCGCCG‑TTTTTTTTCTGTcaca < 1:1269108/139‑1 (MQ=255)
gcaaAAGAGATCCTTAGCGAGATGGGATATACCCACGTTGAGAACGCCGGTGGCCTGAAAGACATCGCAATGCCGAAGGTCAAAGGTTAAAAGAATTCACCATGAGCGGCGCTTATGCGCCG‑TTTTTTTTCTGTCacac > 1:1023928/1‑139 (MQ=255)
tCCTTAGCGAGATGGGATATACCCACGTTGAGAACGCCGGTGGCCTGAAAGACATCGCAATGCCGAAGGTCAAAGGTTAAAAGAATTCACCATGAGCGGCGCTTATGCGCCG‑TTTTTTTTCTGTCACACCTTATTTACa < 2:602621/139‑1 (MQ=255)
tCCTTAGCGAGATGGGATATACCCACGTTGAGAACGCCGGTGGCCTGAAAGACATCGCAATGCCGAAGGTCAAAGGTTAAAAGAATTCACCATGAGCGGCGCTTATGCGCCG‑TTTTTTTTCTGTCACACCTTATTTACa < 2:30198/139‑1 (MQ=255)
ccTTAGCGAGATGGGATATACCCACGTTGAGAACGCCGGTGGCCTGAAAGACATCGCAATGCCGAAGGTCAAAGGTTAAAAGAATTCACCATGAGCGGCGCTTATGCGCCG‑TTTTTTTTCTGTCACACCTTATTTACAt < 2:1023928/139‑1 (MQ=255)
aTGGGATATACCCACGTTGAGAACGCCGGTGGCCTGAAAGACATCGCAATGCCGAAGGTCAAAGGTTAAAAGAATTCACCATGAGCGGCGCTTATGCGCCG‑TTTTTTTTCTGTca < 2:332058/115‑1 (MQ=255)
aTGGGATATACCCACGTTGAGAACGCCGGTGGCCTGAAAGACATCGCAATGCCGAAGGTCAAAGGTTAAAAGAATTCACCATGAGCGGCGCTTATGCGCCG‑TTTTTTTTCTGTca > 1:332058/1‑115 (MQ=255)
aCCCACGTTGAGAACGCCGGTGGCCTGAAAGACATCGCAATGCCGAAGGTCAAAGGTTAAAAGAATTCACCATGAGCGGCGCTTATGCGCCG‑TTTTTTTTCTGTCACACCTTATTTACAT‑CCCCATAGATTATTTGCGt < 1:574168/139‑1 (MQ=255)
gTTGAGAACGCCGGTGGCCTGAAAGACATCGCAATGCCGAAGGTCAAAGGTTAAAAGAATTCACCATGAGCGGCGCTTATGCGCCG‑TTTTTTTTCTGTCACACCTTATTTACAT‑CCCCATAGATTATTTGCGTCAGCTc > 2:949398/1‑139 (MQ=255)
gagaACGCCGGTGGCCTGAAAGACATCGCAATGTCGAAGGTCAAAGGTTAAAAGAATTCACCATGAGCGGCGCTTATGCGCCG‑TTTTTTTTCTGTCACACCTTAtt > 2:1084959/1‑106 (MQ=255)
gagaACGCCGGTGGCCTGAAAGACATCGCAATGCCGAAGGTCAAAGGTTAAAAGAATTCACCATGAGCGGCGCTTATGCGCCG‑TTTTTTTTCTGTcac > 1:238402/1‑98 (MQ=255)
gagaACGCCGGTGGCCTGAAAGACATCGCAATGCCGAAGGTCAAAGGTTAAAAGAATTCACCATGAGCGGCGCTTATGCGCCG‑TTTTTTTTCTGTcac < 2:238402/98‑1 (MQ=255)
gagaACGCCGGTGGCCTGAAAGACATCGCAATGCCGAAGGTCAAAGGTTAAAAGAATTCACCATGAGCGGCGCTTATGCGCCG‑TTTTTTTTCTGTCACACCTTAtt < 1:1084959/106‑1 (MQ=255)
gaACGCCGGTGGCCTGAAAGACATCGCAATGCCGAAGGTCAAAGGTTAAAAGAATTCACCATGAGCGGCGCTTATGCGCCG‑TTTTTTTTCTGTCACACCTTATTTACAT‑CCCCATAGATTATTTGCGTCAGCTCACaaa < 1:949398/139‑1 (MQ=255)
aaCGCCGGTGGCCTGAAAGACATCGCAATGCCGAAGGTCAAAGGTTAAAAGAATTCACCATGAGCGGCGCTTATGCGCCGtttttttt > 2:683002/1‑88 (MQ=255)
aaCGCCGGTGGCCTGAAAGACATCGCAATGCCGAAGGTCAAAGGTTAAAAGAATTCACCATGAGCGGCGCTTATGCGCCGtttttttt < 1:683002/88‑1 (MQ=255)
gCCGGTGGCCTGAAAGACATCGCAATGCCGAAGGTCAAAGGTTAAAAGAATTCACCATGAGCGGCGCTTATGCGCCG‑TTTTTTTTCTGTcac > 1:1258773/1‑92 (MQ=255)
gCCGGTGGCCTGAAAGACATCGCAATGCCGAAGGTCAAAGGTTAAAAGAATTCACCATGAGCGGCGCTTATGCGCCG‑TTTTTTTTCTGTcac < 2:1258773/92‑1 (MQ=255)
ccGGTGGCCTGAAAGACATCGCAATGCCGAAGGTCAAAGGTTAAAAGAATTCACCATGAGCGGCGCTTATGCGCCG‑TTTTTTTTCTGTCACACCTTATTTACAT‑CCCCATAGATTATTTGCGTCAGCTCACAAATACGc > 2:529254/1‑139 (MQ=255)
cGGTGGCCTGAAAGACATCGCAATGCCGAAGGTCAAAGGTTAAAAGAATTCACCATGAGCGGCGCTTATGCGCCGtttttttt < 2:816371/83‑1 (MQ=255)
cGGTGGCCTGAAAGACATCGCAATGCCGAAGGTCAAAGGTTAAAAGAATTCACCATGAGCGGCGCTTATGCGCCGtttttttt > 1:816371/1‑83 (MQ=255)
tGGCCTGAAAGACATCGCAATGCCGAAGGTCAAAGGTTAAAAGAATTCACCATGAGCGGCGCTTATGCGCCG‑TTTTTTTTCTGTCACACCTTATTTACAT‑CCCCATAGATTATTTGCGTCAGCTCACAAATACGCtttt > 1:221235/1‑139 (MQ=255)
tGGCCTGAAAGACATCGCAATGCCGAAGGTCAAAGGTTAAAAGAATTCACCATGAGCAGCGCTTATGCGCCG‑TTTTTTTTCTGTCACACCTTATTTACAT‑CCCCATAGATTATTTGCGTCAGCTCACAAATACGCtttt > 2:368641/1‑139 (MQ=255)
gCCTGAAAGACATCGCAATGCCGAAGGTCAAAGGTTAAAAGAATTCACCATGAGCGGCGCTTATGCGCCG‑TTTTTTTTCTGTCACACCTTATTTACAT‑CCCCATAGATTATTTGCGTCAGCt < 2:1059537/122‑1 (MQ=255)
gCCTGAAAGACATCGCAATGCCGAAGGTCAAAGGTTAAAAGAATTCACCATGAGCGGCGCTTATGCGCCG‑TTTTTTTTCTGTCACACCTTATTTACAT‑CCCCATAGATTATTTGCGTCAGCt > 1:1059537/1‑122 (MQ=255)
aTCGCAATGCCGAAGGTCAAAGGTTAAAAGAATTCACCATGAGCGGCGCTTATGCGCCG‑TTTTTTTTCTGTCACAcc > 2:876281/1‑77 (MQ=255)
aTCGCAATGCCGAAGGTCAAAGGTTAAAAGAATTCACCATGAGCGGCGCTTATGCGCCG‑TTTTTTTTCTGTCACAcc < 1:876281/77‑1 (MQ=255)
aTCGCAATGCCGAAGGTCAAAGGTTAAAAGAATTCACCATGAGCGGCGCTTATGCGCCG‑TTTTTTTTCTGTCACACCTTATTTACATCCCCCATAGATTATTTGCGTCAGCTCACAAATACGCTTTTTCCCTGGTaaaa > 2:454023/1‑139 (MQ=255)
ggTCAAAGGTTAAAAGAATTCACCATGAGCGGCGCTTATGCGCCG‑TTTTTTTTCTGTCACACCTTATTTACATCCCCCATAGATTATTTGCGTCAGCTCACAAATACGCTTTTTCCCTGGTAAAAAATGATTTCCTGCg < 1:454023/139‑1 (MQ=255)
aaGGTTAAAAGAATTCACCATGAGCGGCGCTTATGCGCCGTTTTTTTTTCTGTCACACCTTATTTACAT‑cccc > 1:1427138/1‑73 (MQ=255)
aaGGTTAAAAGAATTCACCATGAGCGGCGCTTATGCGCCGTTTTTTTTTCTGTCACACCTTATTTACAT‑cccc < 2:1427138/73‑1 (MQ=255)
aaGGTTAAAAGAATTCACCATGAGCGGCGCTTATGCGCCG‑TTTTTTTTCTGTCACACCTTATTTACAT‑CCCCATAGATTATTTGCGTCAGCTCACAAATa > 1:564792/1‑100 (MQ=255)
aaGGTTAAAAGAATTCACCATGAGCGGCGCTTATGCGCCG‑TTTTTTTTCTGTCACACCTTATTTACAT‑CCCCATAGATTATTTGCGTCAGCTCACAAATa < 2:564792/100‑1 (MQ=255)
aaaaGAATTCACCATGAGCGGCGCTTATGCGCCG‑TTTTTTTTCTGTCACACCTTa < 1:872251/55‑1 (MQ=255)
aaaaGAATTCACCATGAGCGGCGCTTATGCGCCG‑TTTTTTTTCTGTCACACCTTATTTACAT‑CCCCAt < 2:41201/68‑1 (MQ=255)
aaaaGAATTCACCATGAGCGGCGCTTATGCGCCG‑TTTTTTTTCTGTCACACCTTATTTACAT‑CCCCAt > 1:41201/1‑68 (MQ=255)
aaaaGAATTCACCATGAGCGGCGCTTATGCGCCG‑TTTTTTTTCTGTCACACCTTA‑TTACAT‑CCCCATAGATTATTTGCGTCAGCTCACAAATACGCTTTTTCCCTGGTAAAAAATGATTTCCTGCGTGACTAAAACCCt > 2:1198706/1‑139 (MQ=255)
aaaaGAATTCACCATGAGCGGCGCTTATGCGCCG‑TTTTTTTTCTGTCACACCATa > 2:872251/1‑55 (MQ=255)
cgcTTATGCGCCG‑TTTTTTTTCTGTCACACCTTATTTACAT‑CCCCATAGATTATTTGCGTCAg < 1:822378/63‑1 (MQ=255)
cgcTTATGCGCCG‑TTTTTTTTCTGTCACACCTTATTTACAT‑CCCCATAGATTATTTGCGTCAg > 2:822378/1‑63 (MQ=255)
cgcTTATGCGCCG‑TTTTTTTTCTGTCACACCTTATTTACAT‑CCCCATAGATTATTTGCGTCAGCTCACAAATa < 2:102213/73‑1 (MQ=255)
cgcTTATGCGCCG‑TTTTTTTTCTGTCACACCTTATTTACAT‑CCCCATAGATTATTTGCGTCAGCTCACAAATa > 1:102213/1‑73 (MQ=255)
gcgcCG‑TTTTTTTTCTGTCACACCTTATTTACAT‑CCCCATAGATTATTTGCGTCAGCTCACAAATACGCTTTTTCCCTGGTAAAAAATGATTTCCTGCGTGACTAAAACCCTTGTGCTCAATTGACAGTTTATTTTCTg < 1:529254/139‑1 (MQ=255)
|
AGTCAGGGCAAGCAAAAGAGATCCTTAGCGAGATGGGATATACCCACGTTGAGAACGCCGGTGGCCTGAAAGACATCGCAATGCCGAAGGTCAAAGGTTAAAAGAATTCACCATGAGCGGCGCTTATGCGCCGTTTTTTTTTCTGTCACACCTTATTTACAT‑CCCCATAGATTATTTGCGTCAGCTCACAAATACGCTTTTTCCCTGGTAAAAAATGATTTCCTGCGTGACTAAAACCCTTGTGCTCAATTGACAGTTTATTTTCTG > NC_000913/1369903‑1370169
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
