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 |
|
A3 F54 I1 R1
|
60 |
79.7 |
3402854 |
98.4% |
3348408 |
145.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_002947_CJ‑RC |
5,558,423 |
+GCC |
intergenic (‑84/+87) |
PP_4887 ← / ← PP_4888 |
hypothetical protein/methyl‑accepting chemotaxis transducer |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 5,558,423 | 1 | . | G | 91.7%
| 33.3
/ ‑2.4
| 12 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base G (8/3); total (8/4) |
| Fisher's exact test for biased strand distribution p-value = 3.33e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.41e-01 |
| * | NC_002947_CJ‑RC | 5,558,423 | 2 | . | C | 91.7%
| 33.8
/ ‑2.8
| 12 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base C (8/3); total (8/4) |
| Fisher's exact test for biased strand distribution p-value = 3.33e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.85e-01 |
| * | NC_002947_CJ‑RC | 5,558,423 | 3 | . | C | 91.7%
| 33.7
/ ‑2.8
| 12 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base C (8/3); total (8/4) |
| Fisher's exact test for biased strand distribution p-value = 3.33e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.41e-01 |
GCTGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAG‑‑‑CG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGC > NC_002947_CJ‑RC/5558277‑5558551
|||
gCTGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAg‑‑‑cggc < 7:380314/149‑3 (MQ=255)
aCTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAg‑‑‑cggccccgg < 5:147085/148‑8 (MQ=255)
ggAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAG‑‑‑CGGCCCCGGCAATTTCcg > 7:105376/1‑149 (MQ=255)
ctaTTAGTCGGGCGTAAATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGAATAGCAACACCGCTCTGGTGTGGGTGCGGCCTTGTGTCGCTAATGGGCCGCATAG‑‑‑CGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGgc < 4:162119/146‑1 (MQ=37)
ttAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCTACAGAATAGCAACACCGCTCTGGTGTGGTCGCGGCCTTGTGTCGCTAAAGGGCCGCATAG‑‑‑CGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGgctgc < 8:407229/148‑1 (MQ=255)
cATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAG‑‑‑CGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTc < 8:105376/149‑1 (MQ=255)
cttgtgTCGCCCACAGCATCCCAACCCCGCTCGGGGGGGGGCGCGGCTTGGTGCCGCTAACGGGCCGAATAGGGCCC‑‑‑CCGGCAATTTCCGCGTGTATCCAAAAAACCTGGGGCTGCTATGCAGCCCTTTCGCTACACAAGGCCCACaaa < 8:364893/147‑1 (MQ=255)
ccTTGTGTCGCGAAAGGGCCGCATAG‑‑‑CGGCCCCGGCAATTTACGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGgcgcg > 8:412150/1‑147 (MQ=37)
gtgtCGCGAAAGGGCCGCATAG‑‑‑CGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCt > 2:30764/1‑148 (MQ=255)
tCGCGAAAGGGCCGCATAG‑‑‑CGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGGCCGCGCCGGCGTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgc > 1:309726/1‑149 (MQ=38)
gcgAAAGGGCCGCATAG‑‑‑CGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGcc > 5:59733/1‑88 (MQ=25)
gcgAAAGGGCCGCATAG‑‑‑CGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccg > 4:211084/1‑149 (MQ=255)
gcgAAAGGGCCGCATAG‑‑‑CGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccg > 6:120113/1‑149 (MQ=255)
aGGGCCGCATAG‑‑‑CGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccgc > 8:173397/1‑145 (MQ=255)
|||
GCTGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAG‑‑‑CG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGC > NC_002947_CJ‑RC/5558277‑5558551
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
