Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	76,180	C→T	21.2%	intergenic (+238/‑896)	USA300HOU_0072 → / → USA300HOU_0075	universal stress protein/lysophospholipase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	76,180	0	C	T	21.2%	78.4 / 11.7	44	intergenic (+238/‑896)	USA300HOU_0072/USA300HOU_0075	universal stress protein/lysophospholipase
Reads supporting (aligned to +/- strand):  ref base C (13/19);  new base T (2/7);  total (15/29)
Fisher's exact test for biased strand distribution p-value = 4.45e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

AATTTAATATAACTAATATTGCTGCACCTGTATCACTTAGAACAGCTAACCAAAGTGTTAGTAATCCAGGGAATACTAACACAAAGGCAATTAATTTAATAATTATAGCAAAATATAGGTTCTGTTGCAAAGTTGAATCTATAGTATAATTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAACAATTTAACAAGGATGTTATCACTGTAGCCGTTGGCTACTATCTAAGATATGCATTGAGTTATCGTGATATATCTGAA  >  CP000730/76042‑76313                                                                                                                                           |                                                                                                                                      aaTTTAATATAACTAATATTGCTGCACCTGTATCACTTAGAACAGCTAACCAAAGTGTTAGTAATCCAGGGAATACTAACACAAAGGCAATTAATTTAATAATTATAGCAAAATATAGGTTCTGTTGCAAAGTTGAATCt                                                                                                                                      >  1:35206/1‑140 (MQ=255)            aCTAATATTGCTGCACCTGTATCACTTAGAACAGCTAACCAAAGTGTTAGTAATCCAGGGAATACTAACACAAAGGCAATTAATTTAATAATTATAGCAAAATATAGGTTCTGTTGCAAAGTTGAATCTATAGTATAAtt                                                                                                                           >  1:257309/1‑140 (MQ=255)              taattatgcagcACCTGTAACAACTAGAACAGCTAACCAAATTGTTAGTAATCCAGGGAATACTAACACAAAGGCAATTAATTTAATAAGTATAGCAAAATATAGGTTCTGTTGCAAAGTTGAATCTATAGTATAAtttt                                                                                                                         <  1:30539/134‑1 (MQ=255)                  atTGCTGCACCTGTATCACTTAGAACAGCTAACCAAAGTGTTAGTAATCCAGGGAATACTAACACAAAGGCAATTAATTTAATAATTATAGCAAAATATAGTTTCTGTTGCAAAGTTGAATCTATAATATAATTTTAACa                                                                                                                     >  1:104688/1‑140 (MQ=255)                             cgcaccACTTAGAACACCTAACCAAAGCGTTAGTAATCCAGGGAATACTAACACAAAGGCAATTAATTTAATAATTATAGCAAAATATAGGTTCTGTTGCAAAGTTGAATCTATAGTATAATTTTAaaaaaaccgagcct                                                                                                          <  2:276865/135‑9 (MQ=38)                               tATCACTTAGAACAGCTAACCAAAGTGTTAGTAATCCAGGGAATACTAACACAAAGGCAATTAATTTAATAATTATAGCAAAATATAGGTTCTGTTGCAAAGTTGAATCTATAGTATAATTTTAACAAAAAGGAGtcttc                                                                                                        >  1:175281/1‑140 (MQ=255)                                     ttAGAACAGCTAACCAAAGTTTTAGTAATCCAGGGAATACTAACACAAAGGCAATTAATTTAATAATTATAGCAAAATATAGGTTCTGTTGCAAAGTTGAATCTATAGTATAATTTTAACAAATAGGAGTCTTCTGTATg                                                                                                  <  1:159107/140‑1 (MQ=255)                                     ttAGAACAGCTAACCAAAGTGTTAGTAATCCAGGGAATACTAACACAAAGGCAATTAATTTAATAATTATAGCAAAATATAGGTTCTGTTGCAAAGTTGAATCTATAGTATAATTTTAACAAAAAGGAGTCTTCTGTATg                                                                                                  <  1:292933/140‑1 (MQ=255)                                                aaCCAAATGTTTATTAATCCAAGGAATACTAACACAAATGCAATTAATTTAATAATTATAGCAAAATATAGGTTCTGTTGCAAAGTTGAATCTATAGTATAATTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCAg                                                                                       <  2:37187/140‑1 (MQ=25)                                                  ccAAAGTGTTAGTAATCAAGGGAATACTAACACAAAGGCAATTAATTTAATAATTATAGCAAAATATAGGTTCTGTTGCAAAGTTGAATCTATAGTATAATTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGat                                                                                     <  1:239441/140‑1 (MQ=255)                                                     aaGTGTTAGTAATCCAGGGAATACTAACACAAAGGCAATTAATTTAATAATTATAGCAAAATATAGGTTCTGTTGCAAAGTTGAATCTATAGTATAATTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGAtata                                                                                  >  1:272500/1‑140 (MQ=255)                                                       gtgtTAGTAATTCAGGGAATACTAACACAAAGGCAATTAATTTCATAATAAGAGCAAAATATAGGTTCTGTTGCAAAGTTGAATGTATAGTATAATTAAAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATaaa                                                                                <  2:239156/140‑1 (MQ=21)                                                       gtgtTAGTAATCCAGGGAATACTAACACAAAGGCAATTAATTTAATAATTATAGCAAAATATAGGTTCTGTTGCAAAGTTGAATCTATAGTATAATTTAAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATaaa                                                                                <  2:81817/140‑1 (MQ=255)                                                            agtattccctggattACTAACACAAAGGCAATTAATTTAATAATTATAGCAAAATATAGGTTCTGTTGCAAAGTTGAATCTATAGTATAATTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAACAAtt                                                                           >  2:120218/15‑140 (MQ=21)                                                                   cAGGGAATACTAACACAAAGGCAATTAATTTAATAATTATAGCAAAATATAGGTTCTGTTGCAAAGTTTAATCTATAGTATAATTTTAACAAAAAGGAGACTTCTGTATGAACTATTTACGTAATAAAAAATATAAAAAg                                                                    >  1:128473/1‑140 (MQ=25)                                                                    aGGGAATACTAACACAAAGGCAATTAATTTAATAATTATAGCAAAATATAGGTTCTGTTGCAAAGTTGAATCTATAGTATAATTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAACAATTTAACAAgg                                                                   <  1:133304/140‑1 (MQ=255)                                                                     gggAATACTAACACAAAGGCAATTAAATTAATAATTATAGCAAAATATAGGTTCTGTTGCAAAGTTGAATCTATAGTATAATTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAACAATTTAACAAGGa                                                                  <  2:135273/140‑1 (MQ=255)                                                                      ggAATACTAACACAAAGGCAATTAATTTAATAATTATAGCAAAATATAGGTTCTGTTGCAAAGTTGAATCTATAGTATAATTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAACAATTTAACAAGGAt                                                                 >  2:229671/1‑140 (MQ=255)                                                                               acacAAAGGCAATTAATTTAATAATTATAGCAAAATATAGGTTCTGTTGCAAAGTTGAATCTATAGTATAATTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAACAATTTAACAAGGATGTTATCACt                                                        >  1:15457/1‑140 (MQ=255)                                                                                 acaAAGGGAATTAATTTAATAATTATAGAAACATATAGGTTCTGTTGCAAAGTTGAATCTATAGTATAAAAAAAAAAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAACAATTTAACAAGGATGTTATCACTGt                                                      <  2:318141/140‑1 (MQ=17)                                                                                     aGGCAATTAATTTAATAATTATAGCAAAATATAGGTTCTGTTGCAAAGTTGAATCTATAGTATAATTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAACAATTTAACAAGGATGTTATCACTGTAGcc                                                  <  1:85714/140‑1 (MQ=255)                                                                                         aattaattTAATAATTATAGCAAAATATAGGTTCTGTTGCAAAGTTGAATCTATAGTATAATTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAACAATTTAACAAGGATGTTATCACTGTAGCCGTTg                                              <  2:290795/140‑1 (MQ=255)                                                                                          attaattTAATAATTATAGCAAAATATAGGTTCTGTTGCAAAGTTGAATCTATAGTATAATTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAACAATTTAACAAGGATGTTATCACTGTAGCCGTTgg                                             >  1:8750/1‑140 (MQ=255)                                                                                                  aataatTATAGCAAAATATAGGTTCTGTTGCAAAGTTGAATCTATAGTATAATTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAACAATTTAACAAGGATGTTATCACTGTAGCCGTTGGCTACTATc                                     >  1:151854/1‑140 (MQ=255)                                                                                                              atataggaGGTTCTGTTGCAAAGTTGAATTTATAATATAAGTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAACAATTTAACGAGGATGTTATCACTGTAGCCGTTGGCTACTATCTAAGATATGCAt                         <  2:11328/133‑1 (MQ=11)                                                                                                              agttaggaGGTTCTGTTGCAAAGTTGAATTTATAATATAATTTTAAAAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAACAATTTAACAAGGATGTTATCACTGTATCCGTTGGATACTATCTCAGCTATGCAt                         >  2:186580/8‑140 (MQ=11)                                                                                                                ttaggaGGTTCTGTTGCAAAGTTGAATTTATAATATAATTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAACAATTTAACAAGGATGTTATCACTGTAGCCGTTGGCTACTATCTAAGATATGCATTg                       <  1:70295/135‑1 (MQ=255)                                                                                                                aaatgaGGTTCTGTTGAAAAGTTGAATTTATAGTATAACTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAACAATTTAACAAGGATGTTATCACTGTAGCTGTTGGCTACTATCTAAGATATGCATTg                       <  1:26498/135‑1 (MQ=11)                                                                                                                aaTATAGGTTCTGTTGCAAAGTTGAATCTATAGTATAATTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAACAATTTAACAAGGATGTTATCACTGTAGCCGTTGGCTACTATCTAAGATATGCATTg                       <  2:36338/140‑1 (MQ=40)                                                                                                                aaTATAGGTTCTGTTGCAAAGTTGAATCTATAGTATAATTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAACAATTTAACAAGGATGTTATCACTGTAGCCGTTGGCTACTATCTAAGATATGCATTg                       <  2:36335/140‑1 (MQ=40)                                                                                                                 aatgaGGTTCTGTTGCAAAGTTGAATTTATAGTATAATTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAACAATTTAACAAGGATGTTATCACTGTAGCTGTTGGCTACTATCTAAGATATGCATTGa                      <  1:9737/136‑1 (MQ=9)                                                                                                                  tataGGTTCTGTTGCAAAGTTGAATCTATAGTATAATTTTGACAAAACGGAGTCTTCTGTATGAACTATTTCAGATATAAACAATTTAACAAGGATGTTATCACTGTAGCCGTTGGCTACTATCTAAGATATGCATTGAg                     >  2:207613/1‑140 (MQ=255)                                                                                                                  tataGGTTCTGTTGCAAAGTTGAATCTATAGTATAATTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAACAATTTAACAAGGATGTTATCACTGTAGCCGTTGGCTACTATCTAAGATATGCATTGAg                     <  2:35206/140‑1 (MQ=40)                                                                                                                  atgaGGTTCTGTTGCAAAGTTGAATTTATAGTATAATTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAACAATTTAACAAGGATGTTATCACTGTAGCTGTTGGCTACTATCTAAGATATGCATTGAg                     <  1:202561/137‑1 (MQ=9)                                                                                                                  aggaGGTTCTGTTGCAAAGTTTAATTTATAATATAATTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAACAATTTAACAAGGATGTTATCACTGTAGCCGTTGGCTACTATCTAAGATATGCATTGAg                     <  2:253436/137‑1 (MQ=255)                                                                                                                    actgTTCTGTTGCAAAGTTGAATTTATAATATAATTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAACAATTTAACAAGGATGTTATCACTGTAGCCGTTGGCTACTATCTAAGATATGCATTGAgct                   <  2:112362/137‑3 (MQ=2)                                                                                                                     aGGTTCTGTTGCAAAGTTGAATTTATAGTATAATTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAACAATTTAACAAGGATGTTATCACTGTAGCTGTTGGCTACTATCTAAGATATGCATTGAGTTa                  >  1:111098/1‑140 (MQ=11)                                                                                                                         tCTTTTGCAAAGTTGAATATATAATATAATTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCTGATATAAATAAGTTAACACGGATGTTATCACTGTAGCAGTTGGCTACTATCTAAGATATGCATTGAGCTATCGt              <  2:82011/140‑1 (MQ=11)                                                                                                                           tGTTGCAAAGTTGAATCTATAGTATAATTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAACAATTTAACAAGGATGTTATCACTGTAGCCGTTGGCTACTATCTAAGATATGCATTGAGTTATCGTGa            <  2:8750/140‑1 (MQ=35)                                                                                                                             ttacAAAATTAAATATAAAGAAAAATATAAACAAAAAAGAGTCTACTGTATGAACTATTTCAGATATAAACAATTTAACAAGGATGTTATCACTGTAGCTGTTGGCTACTATCTAAGATATGCATTGAGTTATCGTGata          <  1:23978/137‑1 (MQ=11)                                                                                                                                 aaaGTTGAATCTATAGTATAATTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAACAATTTAACAAGGATGTTATCACTGTAGCCGTTGGCTACTATCTAAGATATGCATTGAGTTATCGTGATATATc      <  1:229671/140‑1 (MQ=37)                                                                                                                                   aGTTGAATCTATAATATAAATATAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAACAATTTAACAAGGATGTTATCACTGTAGCCGTTGGCTACTATCTAAGATATGCATTGAGCTATCGTGATATATCTg    <  2:222084/140‑1 (MQ=255)                                                                                                                                    gTTGAATCTATAGTATAATTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAACAATTTAACAAGGATGTTATCACTGTAGCCGTTGGCTACTATCTAAGATATGCATTGAGTTATCGTGATATATCTGa   <  1:120218/140‑1 (MQ=35)                                                                                                                                     ttGAATCTATAGTATAATTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAACAATTTAACAAGGATGTTATCACTGTAGCCGTTGGCTACTATCTAAGATATGCATTGAGTTATCGTGATATATCTGaa  >  1:13899/1‑140 (MQ=35)                                                                                                                                           |                                                                                                                                      AATTTAATATAACTAATATTGCTGCACCTGTATCACTTAGAACAGCTAACCAAAGTGTTAGTAATCCAGGGAATACTAACACAAAGGCAATTAATTTAATAATTATAGCAAAATATAGGTTCTGTTGCAAAGTTGAATCTATAGTATAATTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGATATAAACAATTTAACAAGGATGTTATCACTGTAGCCGTTGGCTACTATCTAAGATATGCATTGAGTTATCGTGATATATCTGAA  >  CP000730/76042‑76313

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: ‑