Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	656,179	C→T	P38S (CCA→TCA)	USA300HOU_RS03135 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	656,179	0	C	T	96.5%	83.3 / NA	29	P38S (CCA→TCA)	USA300HOU_RS03135	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base T (14/14);  minor base A (1/0);  total (15/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTTATTAATAGGAAGTGATAATTATTGCTTTGTGAAACCGAAATTATCAATAAAAATCCGAAATACAGAGTTATTAAGTATGATGATGAGTATTTAATGGTCGATGTAATAAGAACTTGGCTTGTATACTTTTTTCCATTTATTAATTGGTTCATTCCAAAAAGGTGCGCCAAAATTAGTAGAGAAGAGTATGAAAAACTGAACACTGTTAAGCCAGTTAAAAATAAAAATTTTTGGCCTGTTGTAGGAGGAACAATCCTACTAGGTGCT  >  USA300TCH1516_ALE/656044‑656313                                                                                                                                        |                                                                                                                                       tttataaATAGGAAGTGATAATTATTGCATTGTGAAATGGAAATTATAAATAAAAATTCGAAATACAGAGTTATTAAGTATGATGATGAGTATTTAATGGTCGATGTAATAAGAACTTGGCTTGTATACTTTTTTTCAttt                                                                                                                                   <  2:8267/140‑1 (MQ=38)   tattaATAGGAAGTGATAATTATTGCTTTGTGAAACCGAAATTATCAATAAAAATCCGAAATACAGAGTTATTAAGTATGATGATGAGTATTTAATGGTCGATGTAATAAGAACTTGGCTTGTATACTTTTTTACaagtat                                                                                                                                 >  1:276980/1‑136 (MQ=255)     ttaATAGGAAGTGATAATTATTGCTTTGTGAAACCGAAATTATCAATAAAAATCCGAAATACAGAGTTATTAAGTATGATGATGAGTATTTAATGGTCGATGTAATAAGAACTTGGCTTGTATACTTTTTTTCATttatta                                                                                                                               >  1:116078/1‑141 (MQ=255)     ttaATAGGAAGTGATAATTATTGCTTTGTGAAACCGAAATTATCAATAAAAATCCGAAATACAGAGTTATTAAGTATGATGATGAGTATTTAATGGTCGATGTAATAAGAACTTGGCTTGTATACTTTTTTTCATttatta                                                                                                                               >  1:280062/1‑141 (MQ=255)               gTGATAATTATTGCTTTGTGAAACCGAAATTATCAATAAAAATCCGAAATACAGAGTTATTAAGTATGATGATGAGTATTTAATGGTCGATGTAATAAGAACTTGGCTTGTATACTTTTTTTCATTTATTAATTTGTTCAt                                                                                                                     >  2:38452/1‑141 (MQ=255)               gTGAGAATTAATGCTTTGTGAAACCGAAATTATCAATAAAAATCCGAAATACAGAGTTATTAAGTATGATGATGAGTATTTAATGGTCGATGTAATAAGAACTTGGCTTGTATACTTTTTTTCATTTATTAATTGGTTCAt                                                                                                                     <  2:80546/141‑1 (MQ=255)                                    aaCCGAAATTATCAATAAAAATCCGAAATACAGAGTTATTAAGTATGATGATGAGTATTTAATGGTCGATGTAATAAGAACTTGGCTTGTATACTTTTTTTCATTTATTAATTGGTTCATTCCAAAAAGGTGCGCCAAAAt                                                                                                >  1:162253/1‑141 (MQ=255)                                      ccGAAATTATCAATAAAAATCCGAAATACAGAGTTATTAAGTATGATGATGAGTATTTAATGGTCGATGTAATAAGAACTTGGCTTGTATACTTTTTTTCATTTATTAATTGGTTCATTCCAAAAAGGTGCGCCAAAATta                                                                                              >  1:148024/1‑141 (MQ=255)                                         aaaTTATCAATAAAAATCCGAAATACAGAGTTATTAAGTATGATGATGAGTATTTAATGGTCGATGTAATAAGAACTTGGCTTGTATACTTTTTTTCATTTATTAATTGGTTCATTCCAAAAAGGTGCGCCAAAATtagta                                                                                           <  1:241432/141‑1 (MQ=255)                                           aTTATCAATAAAAATCCGAAATACAGAGTTATTAAGTATGATGATGAGTATTTAATGGTCGATGTAATAAGAACTTGGCTTGTATACTTTTTTTCATTTATTAATTGGTTCATTCCAAAAAGGTGCGCCAAAATTAGTaga                                                                                         <  1:70386/141‑1 (MQ=255)                                            ttATCAATAAAAATCCGAAATACAGAGTTATTAAGTATGATGATGAGTATTTAATGGTCGATGTAATAAGAACTTGGCTTGTATACTTTTTTTCATTTCTTAATTGGTTCATTCCAAAAAGTTGCGCCAAAATTAGTagat                                                                                        >  1:14149/1‑140 (MQ=255)                                                     aaaaTCCGAAATACAGAGTTATTAAGTATGATGATGAGTATTTAATGGTCGATGTAATAAGAACTTGGCTTGTATACTTTTTTTCATTTATTAATTGGTTCATTCCAAAAAGGTGCGCCAAAATTAGTAGAGAAGAGTATg                                                                               >  1:86018/1‑141 (MQ=255)                                                      aaaTCCGAAATACAGAGTTATTAAGTATGATGATGAGTAGTTAATGGTCGATGCAATAAGAACTTGGCTTGTATACTTTTTTTCATTTATTAATTGGTTCATTCCAAAAAGGTGCGCCAAAATTAGTAGAGAAGAGTATGa                                                                              <  1:250789/141‑1 (MQ=255)                                                        aTCCGAAATACAGAGTTATTAAGTATGATGATGAGTATTTAATGGTCGATGTAATAAGAACTTGGCTTGTATACTTTTTTTCATTTATTAATTGGTTCATTCCAAAAAGGTGCGCCAAAATTAGTAGAGAAGAGTATGaaa                                                                            >  1:237781/1‑141 (MQ=255)                                                                           taAGTATGATGATGAGTATTTAATGGTCGATGTAATAAGAACTTGGCTTGTATACTTTTTTTCATTTATTAATTGGTTCATTCCAAAAAGGTGCGCCAAAATTAGTAGAGAAGAGTATGAAAAACTGAACACTGTTAAGcc                                                         >  1:148145/1‑141 (MQ=255)                                                                             aGTATGATGATGAGTATTTAATGGTCGATGTAATAAGAACTTGGCTTGTATACTTTTTTTCTTTTATTAATTGGTTCATTCCAAAAAGGTGTTCTAAATTTAGTAGAGAAGAGTATGAAAAACTGAACACTTTTAAGCCat                                                       >  2:239774/1‑140 (MQ=37)                                                                                         aGTATTTAATGGTCGATGTAATAAGAACTTGGCTTGTATACTTTTTTTCATTTATTAATTGGTTCATTCCAAAAAGGTGCGCCAAAATTAGTAGAGAAGAGTATGAAAAACTGAACACTGTTAAGCCAGTtaaaaataaaa                                           <  2:162253/141‑1 (MQ=255)                                                                                          gTATTTAATGGTCGATGTAATAAGAACTTGGCTTGTATACTTTTTTTCATTTATTAATTGGTTCATTCCAAAAAGGTGCGCCAAAATTAGTAGAGAAGAGTATGAAAAACTGAACACTGTTAAGCCAGTtaaaaataaaaa                                          >  1:17405/1‑141 (MQ=255)                                                                                          gTATTTAATGGTAGATGTAATAAGAACTTGGCTTGTATATTTTTTTTAATTTATTAATTGGTTAATTCCAAAAAGGTGCGCTAAAATTAGTAGAGAAGAGTATGAAAAACTGAACACTGTTAAGCCAGTtaaaaataaaaa                                          <  2:250999/141‑1 (MQ=255)                                                                                                    gTCGATGTAATAAGAACTTGGCTTGTATACTTTTTTTCATTTATTAATTGGTTCATTCCAAAAAGGTGCGCCAAAATTAGTAGAGAAGAGTATGAAAAACTGAACACTGTTAAGCCAGTTAAAAATAAAAATTTTTGGCCt                                <  2:237781/141‑1 (MQ=255)                                                                                                          gTAATAAGAACTTGGCTTGTATACTTTTTTTCATTTATTAATTGGTTCATTCCAAAAAGGTTCTCTAAAATTAGTAGAGAAGAGTATGAAAAACTGAACACTGTTAACACAGTTACAAATAAAAATTTTTGGCCTGTTGTa                          >  2:47473/1‑141 (MQ=38)                                                                                                                  aaCTTGGCTTGTATACTTTTTTTCATTTATTAATTGGTTCATTCCAAAAAGGTGCGCCAAAATTAGTAGAGAAGAGTATGAAAAACTGAACACTGTTAAGCCAGTTAAAAATAAAAATTTTTGGCCTGTTGTAGGAGGAAc                  >  1:199145/1‑141 (MQ=255)                                                                                                                     ttGGCTTGTATACGTTTTTTCATTTATTAATTGGTTCATTCCAAAAAGGTGCGCCAAAATTAGTAGAGAAAAGTATGAAAAACTGAACACTGTTAAGCCAGTTAAAAATAAAAATTTTTGGCCTGTTGTAGGAGGAACAAt               <  2:39512/141‑1 (MQ=255)                                                                                                                      tGGCTTGTATACTTTTTTTCATTTATTAATTGGTTCATTCCAAAAAGGTGCGCCAAAATTAGTAGAGAAGAGTATGAAAAACTGAACACTGTTAAGCCAGTTAAAAATAAAAATTTTTGGCCTGTTGTAGGAGGAACAATc              <  1:3637/141‑1 (MQ=255)                                                                                                                        gCTTGTATACTTTTTTTCATTTATTAATTGGTTCATTCCAAAAAGGTGCGCCAAAATTAGTAGAGAAGAGTATGAAAAACTGAACACTGTTAAGCCAGTTAAAAATAAAAATTTTTGGCCTGTTGTAGGAGGAACAATCct            <  1:182219/141‑1 (MQ=255)                                                                                                                          ttGTATACTTTTTTTCATTTATTAATTGGTTCATTCCAAAAAGGTGCGCCAAAATTAGTAGAGAAGAGTATGAAAAACTGAACACTGTTAAGCCAGTTAAAAATAAAAATTTTTGGCCTGTTGTAGGAGGAACAATCctac          >  1:84572/1‑141 (MQ=255)                                                                                                                              ataCTTTTTTTCATTTATTAATTGGTTCATTCCAAAAAGGTGCGCCAAAATTAGTAGAGAAGAGTATGAAAAACTGAACACTGTTAAGCCAGTTAAAAATAAAAATTTTTGGCCTGTTGTAGGAGGAACAATCCTACTAgg      <  2:116078/141‑1 (MQ=255)                                                                                                                              ataCTTTTTTTCATTTATTAATTGGTTCATTCCAAAAAGGTGCGCCAAAATTAGTAGAGAAGAGTATGAAAAACTGAACACTGTTAAGCCAGTTAAAAATAAAAATTTTTGGCCTGTTGTAGGAGGAACAATCCTACTAgg      <  2:280062/141‑1 (MQ=255)                                                                                                                                  ttttttTCATTTATTAATTGGTTCATTCCAAAAAGGTGCGCCAAAATTAGTAGAGAAGAGTATGAAAAACTGAACACTGTTAAGCCAGTTAAAAATAAAAATTTTTGGCCTGTTGTAGGAGGAACAATCCTACTAGGTGCt  <  2:86018/141‑1 (MQ=255)                                                                                                                                        |                                                                                                                                       GTTATTAATAGGAAGTGATAATTATTGCTTTGTGAAACCGAAATTATCAATAAAAATCCGAAATACAGAGTTATTAAGTATGATGATGAGTATTTAATGGTCGATGTAATAAGAACTTGGCTTGTATACTTTTTTCCATTTATTAATTGGTTCATTCCAAAAAGGTGCGCCAAAATTAGTAGAGAAGAGTATGAAAAACTGAACACTGTTAAGCCAGTTAAAAATAAAAATTTTTGGCCTGTTGTAGGAGGAACAATCCTACTAGGTGCT  >  USA300TCH1516_ALE/656044‑656313

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑