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
A5 F91 I0 R1 918 53.4 2573728 94.2% 2424451 136.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 1,647,971 Δ1 bp 34.6% coding (793/1335 nt) oprB‑II ← carbohydrate‑selective porin

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029471,647,9710A.34.6% 50.3 / 29.9 26coding (793/1335 nt)oprB‑IIcarbohydrate‑selective porin
Reads supporting (aligned to +/- strand):  ref base A (8/9);  new base . (4/5);  total (12/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.50e-01

CTGGTCGGACGCCAGCGAGGTGACCTGCTGCTGGGCGCCAATCCACAAGCCGTGCTTGCTCGAACTGCTGCGGTAGGCGGCGCCGCTGAGGGCGGCCGGCTGACCGTTGCTGTCCTTGAGAACATCTTGTGCCTTGGCATTACTGTAGTAGTAGCCGGCACGATATTCCCCTTTCAAGCCTTGGATACGTGGGGTCCATACCAGTTCGAACGGCATTACCGCACCCTGGGTGCCGCTGCCGCTGAGCTTGAAACCATTGCCGGATTCGAGGTTGGAAGGGTTCTGCTCGAA  >  NC_002947/1647822‑1648112
                                                                                                                                                     |                                                                                                                                             
cTGGTCGGACGCCAGCGAGGTGACCTGCTGCTGGGCGCCAATCCACAAGCCGTGCTTGCTCGAACTGCTGCGGTAGGCGGCGCCGCTGAGGGCGGCCGGCTGACCGTTGCTGTCCTTGAGAACATCTTGTGCCTTGGCATTACTgtagta                                                                                                                                               <  1:350870/150‑1 (MQ=255)
         cGCCAGCGAGGTGACCTGCTGCTGGGCGCCAATCCACAAGCCGTGCTTGCTCGAACTGCTGCGGTAGGCGGCGCCGCTGAGGGCGGCCGGCTGACCGTTGCTGTCCTTGAGAACATCTTGTGCCTTGGCATTACTGTAGTAGTAGCCGGc                                                                                                                                      <  2:119211/150‑1 (MQ=255)
           ccAGCGAGGTGACCTGCTGCTGGGCGCCAATCCACAAGCCGTGCTTGCTCGAACTGCTGCGGTAGGCGGCGCCGCTGAGGGCGGCCGGCTGACCGTTGCTGTCCTTGAGAACATCTTGTGCCTTGGCATTACTGTAGT‑GTAGCCGGCACg                                                                                                                                   >  1:338529/1‑150 (MQ=255)
                                         tCCACAAGCCGTGCTTGCTCGAACTGCTGCGGTAGGCGGCGCCGCTGAGGGCGGCCGGCTGACCGTTGCTGTCCTTGAGAACATCTTGTGCCTTGGCATTACTGTAGTAGTAGCCGGCACGATATTCCCCTTTCAAGCCTTGGATACGTg                                                                                                      <  2:285069/150‑1 (MQ=255)
                                          ccACAAGCCGTGCTTGCTCGAACTGCTGCGGTAGGCGGCGCCGCTGAGGGCGGCCGGCTGACCGTTGCTGTCCTTGAGAACATCTTGTGCCTTGGCATTACTGTAGT‑GTAGCCGGCACGATATTCCCCTTTCAAGCCTTGGATACGTggg                                                                                                    <  1:480295/150‑1 (MQ=255)
                                                   gTGCTTGCTCGAACTGCTGCGGTAGGCGGCGCCGCAAAGGGCGGCCGGCTGACCGTTGCTGTCCTTGAGAACATCTTGTGCCTTGGCAGTACTGTAGTAGTAGCCGGCACGATATTCCCCTTTCAAGCCTTGGATGCGTGGGGTCCATAc                                                                                            >  1:1054712/1‑150 (MQ=255)
                                                           tCGAACTGCTGCGGTAGGCGGCGCCGCTGAGGGCGGCCGGCTGACCGTTGCTGTCCTTGAGAACATCTTGTGCCTTGGCATTACTGTAGTAGTAGCCGGCACGATATTCCCCTTTCAAGCCTTGGATACGTGGGGTCCATACCAGTTCGa                                                                                    >  2:1142156/1‑150 (MQ=255)
                                                           tCGAACTGCTGCGGTAGGCGGCGCCGCTGAGGGCGGCCGGCTGACCGTTGCTGTCCTTGAGAACATCTTGTGCCTTGGCATTACTGTAGT‑GTAGCCGGCACGATATTCCCCTTTCAAGCCTTGGATACGTGGGGTCCATACCAGTTCGaa                                                                                   >  1:808334/1‑150 (MQ=255)
                                                                 tgctgcGGTAGGCGGCGCCGCTGAGGGCGGCCGGCTGACCGTTGCTGTCCTTGAGAACATCTTGTGCCTTGGCATTACTGTAGTAGTAGCCGGCACGATATTCCCCTTTCAAGCCTTGGATACGTGGGGTCCATACCAGTTCGAACGGCa                                                                              >  2:287530/1‑150 (MQ=255)
                                                                     ggtggaGGCGGCGCCGCTGAGGGAGGCAGGAAGACCGTTGCTGTTCTTTAGAACATCTTGTGCCTTGGCATTACTGTAGT‑GTAGCCGGCACGATATTCCCCTTTCAAGCCTTGGATACGTGGGGTCCATACCAGTTCGAACGGCATTAcc                                                                         <  2:1174165/145‑1 (MQ=255)
                                                                     gcGGTAGGCGGCGCCGCTGAGGGCGGCCGGCTGACCGTTGCTGTCCTTGAGAACATCTTGTGCCTTGGCATTACTGTAGTAGTAGCCGGCACGATATTCCCCTTTCAAGCCTTGGATACGTGGGGTCCATACCAGTTCGAACGGCATTAc                                                                          >  2:322605/1‑150 (MQ=255)
                                                                                 gccgcTGAGGGCGGCCGGCTGACCGTTGCTGTCCTTGAGAACATCTTGTGCCTTGGCATTACTGTAGTAGTAGCCGGCACGATATTCCCCTTTCAAGCCTTGGATACGTGGGGTCCATACCAGTTCGAACGGCATTACCGCACCCTGGGt                                                              >  2:435253/1‑150 (MQ=255)
                                                                                              gccggcTGACCGTTGCTGTCCTTGAGAACATCTTGTGCCTTGGCATTACTGTAGT‑GTAGCCGGCACGATATTCCCCTTTCAAGCCTTGGATACGTGGGGTCCATACCAGTTCGAACGGCATTACCGCACCCTGGGTGCCGCTGCCGCTGa                                                <  2:338529/150‑1 (MQ=255)
                                                                                               ccggcTGACCGTTGCTGTCCTTGAGAACATCTTGTGCCTTGGCATTACTGTAGTAGTAGCCGGCACGATATTCCCCTTTCAAGCCTTGGATACGTGGGGTCCATACCAGTTCGAACGGCATTACCGCACCCTGGGTGCCGCTGCCGCTGa                                                <  1:1024683/150‑1 (MQ=255)
                                                                                                cggcTGACCGTTGCTGTCCTTGAGAACATCTTGTGCCTTGGCATTACTGTAGT‑GTAGCCGGCACGATATTCCCCTTTCAAGCCTTGGATACGTGGGGTCCATACCAGTTCGAACGGCATTACCGCACCCTGGGTGCCGCTGCCGCTGAGc                                              <  2:808334/150‑1 (MQ=255)
                                                                                                 ggcTGACCGTTGCTGTCCTTGAGAACATCTTGTGCCTTGGCATTACTGTAGTAGTAGCCGGCACGATATTCCCCTTTCAAGCCTTGGATACGTGGGGTCCATACCAGTTCGAACGGCATTACCGCACCCTGGGTGCCGCTGCCGCTGAGc                                              >  2:1205078/1‑150 (MQ=255)
                                                                                                         gTTGCTGTCCTTGAGAACATCTTGTGCCTTGGCATTACTGTAGTAGTAGCCGGCACGATATTCCCCTTTCAAGCCTTGGATACGTGGGATCCATACCAGTTCGCACGGGATTACGGCACCCTGGGTGCCGCTGCCGCTGAGCTTGaaagc                                      >  1:170163/1‑148 (MQ=255)
                                                                                                              agTCCTGGAGAACATCTTGTGCCTTGGCATTCCTGTAGCAGCGAACGTCTCGTGATTCCCCTTTCAAGGCTAGATTGCTGGGGGTCCATACCAGTTCGAACGGCATTACCGCACCCTGGGTGCCGCTGCCGCTGAGCTTGAAACCATTGc                                 <  1:287530/149‑1 (MQ=255)
                                                                                                                      agaACATCTTGTGCCTTGGCATTACTGTAGTAGTAGCCGGCACGATATTCCCCTTTCAAGCCTTGGATACGTGGGGTCCATACCACTTCGAACGGCATTACCGCACCCTGGGTGCCGCTGCCGCTGAGCTTGAAACCATTGCCGGATTCg                         >  1:554657/1‑150 (MQ=255)
                                                                                                                       gaACATCTTGTGCCTTGGCATTACTGTAGT‑GTAGCCGGCACGATATTCCCCTTTCAAGCCTTGGATACGTGGGGTCCATACCAGTTCGAACGGCATTACCGCACCCTGGGTGCCGCTGCCGCTGAGCTTGAAACCATTGCCGGATTCGAg                       >  2:711037/1‑150 (MQ=255)
                                                                                                                            tCTTGTGCCTTGGCATTACTGTAGTAGTAGCCGGCACGATATTCCCCTTTCAAGCCTTGGATACGTGGGGTCCATACCAGTTCGAACGGCATTACCGCACCCTGGGTGCCGCTGCCGCTGAGCTTGAAACCATTGCCGGATTCGAGGTTg                   <  1:435253/150‑1 (MQ=255)
                                                                                                                            tCTTGTGCCTTGGCATTACTGTAGTAGTAGCCGGCACGATATTCCCCTTTCAAGCCTTGGATACGTGGGGTCCATACCAGTTCGAACGGCATTACCGCACCCTGGGTGCCGCTGCCGCTGAGCTTGAAACCATTGCCGGATTCGAGGTTg                   <  1:150784/150‑1 (MQ=255)
                                                                                                                                          aTTACTGTAGT‑GTAGCCGGCACGATATTCCCCTTTCAAGCCTTGGATACGTGGGGTCCATACCa                                                                                          <  2:917989/64‑1 (MQ=255)
                                                                                                                                          aTTACTGTAGT‑GTAGCCGGCACGATATTCCCCTTTCAAGCCTTGGATACGTGGGGTCCATACCa                                                                                          >  1:917989/1‑64 (MQ=255)
                                                                                                                                             aCTGTAGTAGTAGCCGGCACGATATTCCCCTTTAAAGCCTTGGATACGTGGGGTCCATACCAGTTCGAACGGCATTACCGCACCCTGGGTGCCGCTGCCGCTGAGCTTGAAACCATTGCCGGATTCGAGGTTGGAAGGGTTCTGCTCGaa  <  2:246798/150‑1 (MQ=255)
                                                                                                                                             aCTGTAGTAGTAGCCGGCACGATATTCCCCTGTCCAGCCTTGGATACGTGGGGTCCATACCAGTTCGAACGGCATTACCGCACCCTGGGTGCCGCTGCCGCTGAGCTTGAAACCATTGCCGGATTCGAGGTTGGAAGGGTTCTGCTCGaa  <  1:1096991/150‑1 (MQ=255)
                                                                                                                                             aCTGTAGTAGGAGCCGGCACGATATTCCCCTTTAAAGCCTTGGATACGTGGGGTCCATACCAGTTCGAACGGCATTACCGCACCCTGGGTGCCGCTGCCGCTGAGCTTGAAACCATTGCCGGATTCGAGGTTGGAAGGGTTCTGCTCGaa  <  2:246843/150‑1 (MQ=255)
                                                                                                                                                     |                                                                                                                                             
CTGGTCGGACGCCAGCGAGGTGACCTGCTGCTGGGCGCCAATCCACAAGCCGTGCTTGCTCGAACTGCTGCGGTAGGCGGCGCCGCTGAGGGCGGCCGGCTGACCGTTGCTGTCCTTGAGAACATCTTGTGCCTTGGCATTACTGTAGTAGTAGCCGGCACGATATTCCCCTTTCAAGCCTTGGATACGTGGGGTCCATACCAGTTCGAACGGCATTACCGCACCCTGGGTGCCGCTGCCGCTGAGCTTGAAACCATTGCCGGATTCGAGGTTGGAAGGGTTCTGCTCGAA  >  NC_002947/1647822‑1648112

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A