Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,028,269	G→A	22.2%	P126S (CCA→TCA)	USA300HOU_RS10230 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,028,269	0	G	A	22.2%	46.7 / 8.4	27	P126S (CCA→TCA)	USA300HOU_RS10230	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (7/14);  new base A (2/4);  total (9/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.19e-01

ATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGT‑CGCCAATTCCATGTTG‑AATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTATTAAATAACGCACAATAAGTAATAATAAAAAGACGAACAAGATGA  >  USA300TCH1516_ALE/2028130‑2028409                                                                                                                                              |                                                                                                                                             agaaCCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAAGATGTAGGT‑CGCCAATTCCATGTTG‑AATTTGTACATCTTCCCACTTATATACATAAACTGgt                                                                                                                                             <  1:125340/139‑1 (MQ=255)                ccTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGT‑CGCCAATTCCATGTTG‑AATTTGTACATCTTCCCACTTATATACATAAACTGATGTACGTTGCTCACCa                                                                                                                              >  1:396905/1‑141 (MQ=255)                  tAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGT‑CGCCAATTCCATGTTG‑AATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCaaa                                                                                                                            <  1:381986/141‑1 (MQ=255)                  tAAAATGTGTCTAACAACAATGGTATTATTTTCCGTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGT‑CGCCAATTCCATGTTG‑AATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCaaa                                                                                                                            <  1:382208/141‑1 (MQ=255)                   aaaaCGTGTCTAACAACAATTGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGT‑CGCCAATCCCATGTCG‑AACTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAAc                                                                                                                           <  2:196401/141‑1 (MQ=255)                    aaaTGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTAGGCCCA‑‑CCCTGTGGTAACTTGTGAAGCTTTCCACTTATAGACATAAACTGGTGTACGTTGCTCACCAAAcc                                                                                                                          <  1:316364/141‑1 (MQ=255)                      aTGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGT‑CGCCAATTCCATGTTG‑AATTTGTACATCTTCCCACTTATATACATAAACTGATGTACGTTGCTCACCAAACCAc                                                                                                                        <  1:379242/141‑1 (MQ=255)                                  acaaTGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGT‑CGCCAATTCCATGTTG‑AATTTGTACATCTTCCCACTTATATACATAAACTGATGTACGTTGCTCACCAAACCACTTTTGTTtaata                                                                                                            <  1:411249/141‑1 (MQ=255)                                            gattTTCCTTAATATTTGCAGCTGTTGTTAAGTCAATATGTAGGT‑CGCCAATTCCATGTTG‑AATTTGTACATCTTCCCACTTATATACATAAACTGACGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTg                                                                                                  <  1:243353/140‑1 (MQ=255)                                                   cTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGT‑CGCCAATTCCATGTTG‑AATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCAt                                                                                           >  2:303476/1‑141 (MQ=255)                                                       atatTTGCAGCTTTTGTTAAGTCAATATGTAGGT‑CGCCAATTCCATGTTG‑AATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAAcc                                                                                       <  1:43584/141‑1 (MQ=255)                                                           ttGCAGCTTTTGTTAAGTCAATATGTAGGT‑CGCCAATTCCATGTTG‑AATTTGTACATCTTCCCACTTATATACTTAAACTGATGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCAt                                                                                   >  2:378956/1‑141 (MQ=255)                                                                          aGTCAATATGTAGGT‑CGGCAATTCCATGTTG‑AATTTTTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAACCCACTTTTGTTTAATAAAAGATGGTGCAGTCTTACCCTCATCCGTCGCAACTACtt                                                                    <  2:216119/141‑1 (MQ=255)                                                                              aaTATGTAGGT‑CGCCAATTCCATGTTG‑AATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACtttttt                                                                <  1:283506/141‑1 (MQ=255)                                                                                  tGTAGGT‑CGCCAATTCCATGTTG‑AATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCAGTCGCCACTACTTTTTTTGGt                                                            >  2:368367/1‑141 (MQ=255)                                                                                   gTAGGT‑CGCCAATTCCATGTTG‑AATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGtt                                                           <  1:29697/141‑1 (MQ=255)                                                                                        t‑CGCCAATTCCATGTTG‑AATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAAc                                                      <  2:289504/141‑1 (MQ=255)                                                                                                    aTGTTG‑AATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTATTaa                                           <  2:271084/141‑1 (MQ=255)                                                                                                      gTTG‑AATTTGTACATCTTCACACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTGTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTATTAAAt                                         >  2:27510/1‑141 (MQ=255)                                                                                                       ttG‑AATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTATTAAATa                                        <  1:167112/141‑1 (MQ=255)                                                                                                           aaTTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTATTAAATAACg                                     <  2:144283/141‑1 (MQ=255)                                                                                                            aTTTGGACATCTTCCCACTTATATACATAAAATAGTGTACGTTACTAACCAAAACACTTTTGTTTAATAAAAGATGGTGAAGTTATAACCTCATCCGTCGCAACTAACTTCTTTTAATTATACTTGTTTATTAAATAACGc                                    <  2:135620/141‑1 (MQ=255)                                                                                                                   cATCTTCCCACTTATATACATAGACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTATTAAATAACGCACAATaa                             >  2:287402/1‑141 (MQ=255)                                                                                                                        tCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTATTAAATAACGCACAATAAGtaat                        >  2:239221/1‑141 (MQ=255)                                                                                                                         tccACTTATATACATAAACTGATATACGTGGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTATTAAATAACGCACAATAAGtaata                       <  2:7418/140‑1 (MQ=255)                                                                                                                              ttATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTATTAAATAACGCTCAATCAGTAATAATaaa                  >  1:220201/1‑141 (MQ=255)                                                                                                                                    aCATGAAATGGTGTACGTTGCTCACCAAACCACTTTTGTTTATTAAAAAATGGTGAAGTCATAACCTCATGCGTCGCAACTACTTTTTTTAGTTTAAACTTGTGTATTAGCTTACACTCAATACGTAATAATAagaagagg            >  2:339403/1‑139 (MQ=255)                                                                                                                                          aCTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTAGTAAATAACGTACAATAAGTAATAATAAAAAGACGAACAAg      <  2:397740/141‑1 (MQ=255)                                                                                                                                            gggTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTGTTGGTTTAAACTTGTGTATTAAATAACGCACAATAAGTAATAATAAAAAGACGAACAAgat    <  2:217129/140‑1 (MQ=255)                                                                                                                                             ggTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTCTTTTGGTTTAGACTTGTGTATTAAATAACGCACAATAAGTAATAATAAAAAGACGAACAAgatg   >  1:38543/1‑141 (MQ=255)                                                                                                                                              gtgtACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTATTAAATAACGCACAATAAGTAATAATAAACAGACGAACACgatga  >  1:290275/1‑141 (MQ=255)                                                                                                                                              gtgtACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTATTAAATAACGCACAATAAGTAATAATAAAAAGATGACCAAgaaca  >  2:66498/1‑138 (MQ=255)                                                                                                                                              |                                                                                                                                             ATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGT‑CGCCAATTCCATGTTG‑AATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCATCCGTCGCAACTACTTTTTTTGGTTTAAACTTGTGTATTAAATAACGCACAATAAGTAATAATAAAAAGACGAACAAGATGA  >  USA300TCH1516_ALE/2028130‑2028409

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: ‑