Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	111,512	A→G	28.5%	S194S (TCA→TCG)	USA300HOU_RS00520 →	putative lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	111,512	0	A	G	28.5%	63.1 / 22.3	43	S194S (TCA→TCG)	USA300HOU_RS00520	putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base A (14/16);  new base G (7/5);  total (22/21)
Fisher's exact test for biased strand distribution p-value = 7.34e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTACTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAA  >  USA300TCH1516_ALE/111373‑111651                                                                                                                                            |                                                                                                                                            cTACTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGATGCCGAGTTATTCa                                                                                                                                             >  1:241082/1‑140 (MQ=255)  tACTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGTGCATTATAGCAATTTTAAAGATTTAATGAATTATAAAAGTGGAGATATATCATATAATCCAGATGTGCCGAGCTATTCAg                                                                                                                                            >  2:253480/1‑140 (MQ=21)     tGAGGAAGTTAAATAATAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCta                                                                                                                                         <  1:86002/140‑2 (MQ=255)     tGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTc                                                                                                                                         <  1:205541/140‑1 (MQ=255)            gTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTACCGAGTTATTCAGCTCAATATCa                                                                                                                                  >  1:261481/1‑140 (MQ=255)             ttAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATAGATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCaa                                                                                                                                 >  1:182987/1‑140 (MQ=255)               aaaGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAAtt                                                                                                                               >  1:211503/1‑140 (MQ=255)                      aaaaCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTAAATATCAATTAACTAat                                                                                                                        >  1:13742/1‑140 (MQ=255)                       aaaCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatg                                                                                                                       >  2:242760/1‑140 (MQ=255)                        aaCATAAAAAAAGAAATCGAAAAATTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGACTTATAAAGATGGAGATATATCATATAATCCAGCGGTGCCGAGTTATTTAGCTCAATATTAATTAACTAatga                                                                                                                      >  1:72191/1‑140 (MQ=21)                         aCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAatgat                                                                                                                     >  1:212024/1‑140 (MQ=255)                          cATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatgatg                                                                                                                    >  1:118599/1‑140 (MQ=255)                             aaaaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGAtt                                                                                                                 <  1:286750/140‑1 (MQ=255)                              aaaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATta                                                                                                                >  1:129246/1‑140 (MQ=255)                                 aaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATaa                                                                                                             >  2:98546/1‑140 (MQ=255)                                  aaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAAt                                                                                                            <  1:162415/140‑1 (MQ=255)                                         cGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAAc                                                                                                     <  2:50454/140‑1 (MQ=255)                                            taaCTTTTAGTTTTTTGCGAAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAAt                                                                                                  <  1:288968/139‑1 (MQ=255)                                            aaaCTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCTGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAAt                                                                                                  <  1:139443/140‑1 (MQ=255)                                            aaaCTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAAt                                                                                                  <  1:289059/140‑1 (MQ=255)                                            aaaCTTTAAGTTGTTTGCGAAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAAt                                                                                                  <  1:206922/140‑1 (MQ=17)                                               cTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTAc                                                                                               >  1:206636/1‑140 (MQ=255)                                               cTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTACTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTAc                                                                                               <  2:205680/140‑1 (MQ=255)                                                 ttAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACgc                                                                                             <  2:9414/140‑2 (MQ=255)                                                  tAAGTTTTTTGCGCAATATAGCAATTTTAAAGCTTTCATGAATGATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTa                                                                                            <  1:59384/140‑1 (MQ=255)                                                  tAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTa                                                                                            <  2:250827/140‑1 (MQ=255)                                                    aGTTTATTGTGCAATATCGCAATTTTAAAGAGTTAATGAAATATAAAGATGGAGATATATCATATAGTCCAGAGGTGCCGAGTTATTCGGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCaaa                                                                                          >  1:235632/1‑140 (MQ=17)                                                     gTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTaaaa                                                                                         <  1:254574/140‑1 (MQ=255)                                                            gcgcAATATAGCAATTTTAAAGCTATACTAGTTGATAAAGATGGAGATATATCATATAATCCAGAGTTGCCGAGTTATTCAGCTCAATATCAATTACCTAATGCTGATTATAATGTAAAACAATTACGTAAAAGAAATGa                                                                                  >  1:76510/1‑140 (MQ=17)                                                            gcgcAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGa                                                                                  <  2:312266/140‑1 (MQ=255)                                                                   ataGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATCTAATCTCACTAAAAGGTGACGAAAGCTACTGCTAAATATCAATTAACTACTGATAATTAGAATGTGAAACAATTACGCAAAAGATATGATATAccg                                                                           >  1:75497/1‑139 (MQ=9)                                                                              aaaGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAGCAAATAAAgc                                                                <  1:234543/140‑1 (MQ=255)                                                                               aaGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCACCGAGTAAAgcg                                                               >  2:223163/1‑140 (MQ=11)                                                                                              gtaAAGAGTGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGttcttg                                                <  1:229947/139‑1 (MQ=255)                                                                                                 aaGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGaaa                                             >  2:196398/1‑140 (MQ=255)                                                                                                             tatCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACACATAAAGCGCCGAAGCTGTTGTTGAAGGGAACAGGGaaa                                 >  2:76053/1‑139 (MQ=255)                                                                                                              atCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAAtt                                <  2:162485/140‑1 (MQ=255)                                                                                                               tCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTATAAGCTTTACGTACAAGATACTACAGACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAAttt                               <  1:315454/140‑1 (MQ=17)                                                                                                                  tataATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTaaa                            >  2:35810/1‑140 (MQ=255)                                                                                                                          agatGTGCCGAGTTATTTAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACAGACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAATGTACAGCGAATTTAAAAGGTtcat                    <  2:72191/140‑1 (MQ=17)                                                                                                                              gTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATAATAATGTAAAACAATTACGCAAAAGATATGCTATAACAAAAAATAAAGCGCCGAAGCTATTGTTAAAAAGTACAGAGAATTTAAAAGGTTCATCAGt                >  2:104346/1‑140 (MQ=11)                                                                                                                               tGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGtt               >  2:172516/1‑140 (MQ=255)                                                                                                                                 ccGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTgg             >  2:182099/1‑140 (MQ=255)                                                                                                                                          tCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATaaaaa    <  1:196398/140‑1 (MQ=255)                                                                                                                                            aGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGACAGGTACAGGGAATTTAAAAGGTTCCTCAGTTCGACATgaaaaaa  >  1:319764/1‑140 (MQ=17)                                                                                                                                            |                                                                                                                                            CTACTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAA  >  USA300TCH1516_ALE/111373‑111651

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: ‑