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
A18 F25 I0 R1 17 19.2 625642 96.1% 601241 148.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP009273 3,180,810 G→A 16.8% pseudogene (31/2445 nt) yqiG → pseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0092733,180,8100GA16.8% 46.7 / 3.7 25pseudogene (31/2445 nt)yqiGpseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein
Reads supporting (aligned to +/- strand):  ref base G (6/14);  new base A (2/2);  total (8/17)
Fisher's exact test for biased strand distribution p-value = 5.78e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.61e-01

ATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACGCCAATCC  >  CP009273/3180668‑3180954
                                                                                                                                              |                                                                                                                                                
acaaCGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTATg                                                                                                                                            <  1:92638/147‑1 (MQ=255)
                           tGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGAATTCAACAAAGATTTAATCg                                                                                                                 <  2:234205/149‑1 (MQ=255)
                               ttATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGAATTCAACAAAGCTTTAAGCGCAGc                                                                                                             >  1:187194/1‑149 (MQ=255)
                                    gctcgcCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAACTTATGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAg                                                                                                        >  1:287056/1‑149 (MQ=255)
                                    gctcgcCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAACTTATGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAg                                                                                                        >  1:287058/1‑149 (MQ=255)
                                           aCGGGAATATCTGCGGCAGCGCGCTTGTAGTGGTTTAAGTTGTAACAGATTTCTGGAAATATAGGGGCAAATACAGTTATCATCATTGGTTGTGCGTCGGCTTATGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAGTATCGGGa                                                                                                 >  1:229796/1‑149 (MQ=25)
                                            ttacattatCGGCGGCAGCTGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGAATTAAACATAGATTTAATCGAAGCCGAAGATCGTGaa                                                                                                <  2:295465/143‑1 (MQ=25)
                                                        cGGCCGGGGGCTTGTAAGTGTTTAAGTGGAGACAGGTGTCTGGAAATATAGGGGCAACCCCAGGTAGCATCATGTCTTTTGCTGCACCTGATGCCGTTGAATTCCACAAATAGTTAATCGAATCCGAAGATCGTGAAACCGTTAAccct                                                                                    <  1:86905/149‑3 (MQ=255)
                                                          gCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTc                                                                                  >  1:293390/1‑149 (MQ=255)
                                                           cAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTcc                                                                                 >  2:254280/1‑149 (MQ=255)
                                                                   ttGTGATGGGTTAAGTGAGAACAGATGGCTGGAAATATAGGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTAGGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGa                                                                         <  1:106945/149‑1 (MQ=255)
                                                                     gTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGaaa                                                                       <  1:226347/149‑1 (MQ=255)
                                                                          gggTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCCTATGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGAt                                                                  >  2:58006/1‑149 (MQ=255)
                                                                            gTTAAGTGATAACGGATGGCGGGAAATATAGGGGCAATGCCAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATgg                                                                <  1:45129/149‑1 (MQ=255)
                                                                                agggATAACGGCTGTCTGGAAATACAGGGGCAAATCCAGTCATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGAATTCAACAAAGATTTACTCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCaa                                                            <  1:31038/146‑1 (MQ=255)
                                                                                                       ataGGGGCAAATCCAGGTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTGTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACt                                     <  1:143936/149‑1 (MQ=255)
                                                                                                                aaTCCAGTTAGCATCAGTGGTTGGGCGTCAGCCTCTGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAGCTGATGGCCAATTACCCGTCGGAAAATAATCGCTACGCActct                            <  1:37541/149‑1 (MQ=255)
                                                                                                                   ccAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGAt                         <  2:187194/149‑1 (MQ=255)
                                                                                                                        tATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATtaata                    <  2:210669/149‑1 (MQ=255)
                                                                                                                              catTGGTTGTGCGTCAGCTTATGCAGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAACACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTACGCACTCTGATTAATAATAaga              <  1:198015/149‑1 (MQ=255)
                                                                                                                                 tGGTTGTGCGTCAACTTATGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAACCTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGa           <  2:287058/149‑1 (MQ=255)
                                                                                                                                 tGGTTGTGCGTCAACTTATGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGa           <  2:287056/149‑1 (MQ=255)
                                                                                                                                    ttGTGCGTCAGCTTATGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACGc        <  1:254280/149‑1 (MQ=255)
                                                                                                                                         cGTCAGCTTATGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACGCCAATc   >  2:114872/1‑149 (MQ=255)
                                                                                                                                          gTCAGCTTATGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATTGTGTAAACGTTAACCTTTCCCAATTGTAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTATTAATAAGAGGACGCCAATcc  <  1:108855/149‑1 (MQ=255)
                                                                                                                                              |                                                                                                                                                
ATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACGCCAATCC  >  CP009273/3180668‑3180954

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A