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 |
|
A4 F25 I1 R1
|
60 |
73.8 |
3348830 |
98.7% |
3305295 |
145.5 |
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 | 94.4%
| 54.0
/ ‑5.6
| 18 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/0); major base G (5/12); minor base C (0/1); total (5/13) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| * | NC_002947_CJ‑RC | 5,558,423 | 2 | . | C | 100.0%
| 60.8
/ NA
| 18 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (5/13); total (5/13) |
| * | NC_002947_CJ‑RC | 5,558,423 | 3 | . | C | 100.0%
| 59.7
/ NA
| 18 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (5/13); total (5/13) |
CGCTGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGC > NC_002947_CJ‑RC/5558276‑5558551
|||
cGCTGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAgcg < 3:267381/148‑1 (MQ=255)
cTGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAgcggcc < 5:217691/149‑4 (MQ=255)
tCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAgcggccccg < 5:133551/149‑7 (MQ=255)
tCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAgcggccccg < 6:272629/149‑7 (MQ=255)
aCTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACTGCTCAGGAGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAgcggccccgg > 7:402705/1‑141 (MQ=255)
aCTGTGCAGGAAATTCAGGTCGGCCTAGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAgcggccccgg < 8:393974/148‑8 (MQ=255)
aaaTTCAGGTGGGCCTGGGCAGCTATTTGTCGGGCGTACTTGAGCAACTCATTTTGTCTTTTGTCGCCTACAGCATATCAACACCGCTCTGGTGTGGGAGCGGCCTTGTGTCGCTAAAGGGCCCCATAGCGGCCCCGGCAATTTCcgc < 8:424355/148‑1 (MQ=21)
ttCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCTACAGCATAGCAACACCGCTCAGGGGTGGGAGCGGCCTTGTGTCGCTAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCgtgt < 6:343672/149‑1 (MQ=38)
aGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCTGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTAt < 6:338581/148‑1 (MQ=38)
gTCGGCCTGGTCTGGGATTAGTCGGGCGTAATTGAGAAACTCATTTTGTCTTGTGTCGCCTAAAGAATAGCAACACTGCTCAGGTGTGGGAGCGGCTTTTTGTCGCTAAAGGGCCGAATAGCGGCCCCGGCAATTTCCGCGTGTAt < 8:402705/146‑1 (MQ=255)
gTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGc > 3:349969/1‑148 (MQ=255)
gTCGGCCGGGGCTGTGTTTTGTCGGGGGGACTTCTTCAACTCGTTTTTTTATGTGTCGCCCAAAGAATAGAAACCCGGCTATGGTTTGGGTGCGTCC‑TGTGGCGCTAATGGGCCCAATAGCGGCCCCGGCAATTTCCGCGTGTATGcaa < 4:355176/149‑1 (MQ=255)
ggCTGCGTTTAGTCGGGCGTAATTGAGAAACGCGTTTTGTCTTGTGTCGCCGACTGCATAGAAACACCGCTCTGGTGTGGGAGGGGCGTTGTGTGGCTAAAGGGCCGAATTGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTg < 8:58468/149‑1 (MQ=255)
aGCGATTAGGGGGGCGGACATGACCAACTCTTTTTGTCTGGTGTCGCCTACAGCAAACCAACACCGCTCCGGTGTGGGCGGGGCGTTGTGCCGCTAACGGGCCTATTAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTgggg < 4:173442/149‑1 (MQ=255)
gATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCgtg > 7:151962/1‑128 (MQ=37)
tCGGGCGGAAATGAGCAACTCATTTTGTCTTGTGTCGCCGACTGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCTAAAGGGCCGCATTGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATg < 2:300816/148‑1 (MQ=37)
tCGCGCGGCCATCACCAACTCCTTTTGTCATGTGTCGCCGACAGCATCGCAACCCCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGCCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGc < 4:349969/149‑1 (MQ=37)
ggcttaaaTGAGCAACTCCTTTTTTTATTTTTCGCCTAAAGAATATAAACACCGCTCATTTTTGGGAGCGTCCTTTTGTCGCTAAAGGCCCCAATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGc < 8:127703/142‑1 (MQ=255)
aTGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTTGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTcg > 2:69505/1‑149 (MQ=39)
accAACTCCTTTTGTCATGTGGCCCCGACAGCATAGCAACACCGCGCAGGTGTGGGAGCGGCCTTGTGTCGCTAACGGGCCCCATAGCGCCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTcgcg < 5:379146/146‑1 (MQ=37)
gcTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCTAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTgggg < 4:357968/122‑1 (MQ=37)
ttttGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAgcggc > 7:102391/1‑80 (MQ=255)
ttttGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAgcggc < 8:102391/82‑3 (MQ=255)
ggggcggggCCTTGTGTCGCTAACGGGCCCCATGGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCTACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGc < 6:305974/142‑1 (MQ=255)
aaaGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccgc > 2:178867/1‑147 (MQ=255)
aaGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccgc > 1:134828/1‑146 (MQ=255)
|||
CGCTGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGC > NC_002947_CJ‑RC/5558276‑5558551
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
