Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,373,493	A→T	10.2%	I112I (ATA→ATT)	USA300TCH1516_01283 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,373,493	0	A	T	10.2%	112.9 / 5.1	39	I112I (ATA→ATT)	USA300TCH1516_01283	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (18/17);  new base T (2/2);  total (20/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.10e-01

ATTGGTTTGCTTTTTTCTACAGTTCTAATTTGGACTTCTCGATTTGAAGTCAAAGGTACAGAAATTTATATGAAACGATCTAAAGCATTTCCAGTTATTTTGATTTCATTACTTATCATTCGTACTGTGATGAAAATATTCATTAGTAATGAAATAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTT  >  USA300TCH1516_ALE/1373356‑1373632                                                                                                                                          |                                                                                                                                            aTTGGTTTGCTTTTTTCTACAGTTCTAATTTGGACTTCTCGATTTGAAGTCAAAGGTACAGAAATTTATATGAAACGATCTAAAGCATTTCCAGTTATTTTGATTTCATTACTTATCATTCGTACTGTGATGAAAATAtt                                                                                                                                           <  1:488693/140‑1 (MQ=255)            tttttCTACAGTTCTAATTTGGACTTCTCGATTTGAAGTCAAAGGTACAGAAATTTATATGAAACGATCTAAAGCATTTCCAGTTATTTTGATTTCATTACTTATCATTCGTACTGTGATGAAAATATTCATTAGTAATg                                                                                                                                <  2:453790/140‑1 (MQ=255)               ttCTACAGTTCTAATTTGGACTTCTCGATTTGAAGTCAAAGGTACAGAAATTTATATGAAACGATCTAAAGCATTTCCAGTTATTTTGATTTCATTACTTATCATTCGTACTGTGATGAAAATATTCATTAGTAATGaaa                                                                                                                             >  2:543810/1‑140 (MQ=255)                tCTACAGTTCTAATTTGGACTTCTCGATTTGAAGTCAAAGGTACAGAAATTTATATGAAACGATCTAAAGCATTTCCAGTTATTTTGATTTCATTACTTATCATTCGTACTGTGATGAAAATATTCATTAGTAATGCAAt                                                                                                                            >  1:472508/1‑140 (MQ=255)                   aCAGTTCTAATTTGGACTTCTCGATTTGAAGTCAAAGGTACAGAAATTTATATGAAACGATCTAAAGCATTTCCAGTTATTTTGATTTCATTACTTATCATTCGTACTGTGATGAAAATATTCATTAGTAATGAAATAGa                                                                                                                         >  2:440714/1‑140 (MQ=255)                                   cTTCTCGATTTGAAGTCAAAGGTACAGAAATTTATATGAAACGATCTAAAGCATTTCCAGTTATTTTGATTTCATTACTTATCATTCGTACTGTGATGAAAATATTCATTAGTAATGAAATAGATCCTGGAGAATTAggc                                                                                                         <  2:420776/140‑1 (MQ=255)                                    ttCTCGATTGGAAGTCAAAGGTACAGAAATTTATATGAAACGATCTAAAGCATTTCCAGTTATTTTGATTTCATTACTTATCATTCGTACTGTGATGTAAATATTCATTAGTAATGCAATAGATCCTGGAGAATTAggcg                                                                                                        <  2:302523/140‑1 (MQ=255)                                     tctcGATTTGAAGTCAAAGGTACAGAAATTTATATGAAACGATCTAAAGCATTTCCAGTTATTTTGATTTCATTACTTATCATTCGTACTGTGATGAAAATATTCATTAGTATTGAATTAGATCATGGAGGATTAggcgc                                                                                                       >  2:300053/1‑139 (MQ=255)                                     tctcGATTTGAAGTCAAAGGTACAGAAATTTATATGAAACGATCTAAAGCATTTCCAGTTATTTTGATTTCATTACTTATCATTCGTACTGTGATGAAAATATTCATTAGTAATGAAATAGATCCTGGAGAATTAggcgg                                                                                                       <  1:7657/140‑1 (MQ=255)                                          aTTTGAAGTCAAAGGTAAAGAAATTTGTTCGAAACGATCTAAAGCATTTCCAGTTATTTTGATTTCATTACTTATCATTCGTACTGTGATGAAAATATTCATTAGTAATGAAATAGATCCTGGAGAATTAGGCGGCATGt                                                                                                  <  2:521816/140‑1 (MQ=255)                                               aaGTCAAAGGTACAGAAATTTATATGAAACGATCTAAAGCATTTCCAGTTATTTTGATTTCATTACTTATCATTCGTACTGTGATGAAAATATTCATTAGTAATGAAATAGATCCTGGAGAATTAGGCGGCATGTTCttt                                                                                             >  2:532901/1‑140 (MQ=255)                                                aGTCAAAGGTACAGAAATTTATATGAAACGATCTAAAGCATTTCCAGTTATTTTGATTTCATTACTTATCATTCGTACTGTGATGAAAATATTCATTAGTAATGAAATAGATCCTGGAGAATTAGGCGGCATGTCGtttt                                                                                            >  2:55013/1‑140 (MQ=255)                                                 gTCAAAGGTACAGAAATTTATATGAAACGATCTAAAGCATTTCCAGTTATTTTGATTTCATTACTTATCATTCGTACTGTGATGAAAATATTCATTAGTAATGAAATAGATCCTGGAGAATTAGGCGGCATGTTCttttt                                                                                           <  1:535076/140‑1 (MQ=255)                                                               aaTTTGTGTGAAACGATCTAAAGCATTTTCAGTTAGTGTGATTTCCTTACTTATCAGTCGTACTGTGATGAAAATATTCATTAGTAATGAAATAGATCCTGGAGAATTAGGCGGCATGTTCTTTTCATTAGCATTCTGTa                                                                             <  2:288618/140‑1 (MQ=255)                                                               aaTTTATATGAAACGATCTAAAGCATTTCCAGTTATTTTGATTTCATTACTTATCATTCGTACTGTGATGAAAATATTCATTAGTAATGAAATAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTa                                                                             <  1:87618/140‑1 (MQ=255)                                                                aTTTATATGAAACGATCTAAAGCATTTCCAGTTATTTTGATTTCATTACTTATCATTCGTACTGTGGTGAAAATATTCATTAGTAATGAAATAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTAt                                                                            <  2:436098/140‑1 (MQ=255)                                                                 tttATATGAAACGATCTAAAGCATTTCCAGTTATTTTGATTTCATTACTTATCATTCGTACTGTGATGAAAATATTCATTAGTAATGAAATAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATg                                                                           >  1:416288/1‑140 (MQ=255)                                                                  ttATATGAAACGATCTAAAGCATTTCCAGTTATTTTAATTTCATTACTTATCATTCGTACTGTGATGAAAATATTCATTAGTAATGAATTAGATCCTGGAGAATTAGGCGTCATGTTCTTTTTATTAGCATTATGTATGa                                                                          >  2:82858/1‑140 (MQ=255)                                                                      atGAAACGATCTAAAGCATTTCCAGTTATTTTGATTTCATTACTTATCATTCGTACTGTGATGAAAATATTCATTAGTAATGAAATAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGt                                                                      >  1:553660/1‑140 (MQ=255)                                                                           aCGATCTAAAGCATTTCCAGTTATTTTGATTTCATTACTTATCATTCGTACTGTGATGAAAATTTTCATTAGTAATGAAATAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCtt                                                                 >  1:197074/1‑140 (MQ=255)                                                                           aCGATCTAAAGCATTTCCAGTTATTTTGATTTCATTACTTATCATTCGTACTGTGATGAAAATTTTCATTAGTAATGAAATAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCtt                                                                 >  1:193389/1‑140 (MQ=255)                                                                            cGATCTAAAGCATTTCCAGTTATTTTGATTTCATTACTTATCATTCGTACTGTGATGAAAATATTCATTAGTAATGAAATAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTg                                                                <  1:440714/140‑1 (MQ=255)                                                                               tCTAAAGCATTTCCAGTTATTTTGATTTCATTACTTATCATTCGTACTGTGATGAAAATATTCATTAGTAATGAAATAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGgag                                                             <  2:189849/140‑1 (MQ=255)                                                                                cTAAAGCATTTCCAGTTATTTTGATTTCATTACTTATCATTCGTACTGTGATGAAAATATTCATTAGTAATGAAATAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGgaga                                                            <  1:394260/140‑1 (MQ=255)                                                                                 tAAAGCATTTCCAGTTATTTTGATTTCATTACTTATCATTCGTACTGTGATGAAAATATTCATTAGTAATGAAATAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGagag                                                           >  1:62/1‑140 (MQ=255)                                                                                   aaGCATTTCCAGTTATTTTGATTTCATTACTTATCATTCGTACTGTGATGAAAATATTCATTAGTAATGAAATAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGagca                                                         >  1:471378/1‑140 (MQ=255)                                                                                                            aTTACTTATCATTCGTACTGTGATGAAAATATTCATTAGTAATGAAATAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAAc                                >  2:386934/1‑140 (MQ=255)                                                                                                             ttACTTATCATTCGTACTGTGATGAAAATTTTCATTAGTAATGAAATAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACt                               <  2:193389/140‑1 (MQ=255)                                                                                                             ttACTTATCATTCGTACTGTGATGAAAATTTTCATTAGTAATGAAATAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACt                               <  2:197074/140‑1 (MQ=255)                                                                                                                  tATCATTCGTACTGTGATGAAAATATTCATTAGTAATGAAATAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGa                          >  1:22465/1‑140 (MQ=255)                                                                                                                    tCATTCGTACTGTGATGAAAATATTCATTAGTAATGAAATAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGaaa                        <  1:344131/140‑1 (MQ=255)                                                                                                                     cATTCGTACTGTGATGAAAATATTCATTAGTAATGAAATAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGaaaa                       >  2:359623/1‑140 (MQ=255)                                                                                                                     cATTCGTACTGTGATGAAAATATTCATTAGTAATGAAATAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGaaaa                       >  2:194476/1‑140 (MQ=255)                                                                                                                        tCGTACTGTGATGAAAATATTCATTAGTAATGAAATAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACac                    >  2:64225/1‑139 (MQ=255)                                                                                                                             cTGTGATGAAAATATTCATTAGTAATGAAATAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATc               >  1:67739/1‑140 (MQ=255)                                                                                                                                tgatgaAAATATTCATTAGTAATGAAATAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCaat            <  1:532901/140‑1 (MQ=255)                                                                                                                                     aaaaGATTGATTAGTAATGAAATAGATCATGGAGAATTAGGCTGCATGTTATTTTTATTAGCATTATGTATGATTGTTCCTTAGAGAGCAGAAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCaattaatt       <  2:226732/140‑1 (MQ=255)                                                                                                                                      aaaTATTCATTAGTAATGAAATAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAattaatta      <  1:527347/140‑1 (MQ=255)                                                                                                                                       aaTATTCATTAGTAATGAAATAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTAc     >  1:428324/1‑140 (MQ=255)                                                                                                                                        atatTCATTAGTAATTAAATAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACt    <  2:551475/140‑1 (MQ=255)                                                                                                                                          atTCATTAGTAATGAAATAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACttt  <  1:278855/140‑1 (MQ=255)                                                                                                                                          |                                                                                                                                            ATTGGTTTGCTTTTTTCTACAGTTCTAATTTGGACTTCTCGATTTGAAGTCAAAGGTACAGAAATTTATATGAAACGATCTAAAGCATTTCCAGTTATTTTGATTTCATTACTTATCATTCGTACTGTGATGAAAATATTCATTAGTAATGAAATAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTT  >  USA300TCH1516_ALE/1373356‑1373632

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑