Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,724,706	G→T	13.0%	P192T (CCA→ACA)	alaS ←	Alanine‑‑tRNA ligase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,724,706	0	G	T	13.0%	70.9 / 5.9	31	P192T (CCA→ACA)	alaS	Alanine‑‑tRNA ligase
Reads supporting (aligned to +/- strand):  ref base G (14/13);  new base T (2/2);  total (16/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.66e-02

AGGCCATACGCTCAAGCCCCATGCCAGTATCAATATTTTTATTAGGTAATGGTGTGTAACTATGATCTTTATTATGATTGAATTCACTAAATACTAAGTTCCATACTTCAAGATAGCGTTCATTTTCTCCACCTGGATACATTTCTTCTGCCGGATCGTCTTGTCCATATGCTTCTCCGCGATCATAGAAAATCTCAGTGTTCGGTCCTGAAGGCCCTTCACCAATATCCCAGAAGTTACCTTCAATGCGAATAATACGACTTTCTTCAAGCCCA  >  USA300TCH1516_ALE/1724571‑1724845                                                                                                                                        |                                                                                                                                            aGGCCATACGCTCAAGCCCCATGCCAGTATCAATATTTTTATTAGGTAATGGTGTGTAACTATGATCTTTATTATGATTGAATTCACTAAATACTAAGTTCCATACTTCAAGATAGCGTTCATTTTCTCCACCTGGATACa                                                                                                                                        >  2:205874/1‑141 (MQ=255)                gCCCCATGCCAGTATCAATATTTTTATTAGGTAATGGTGTGTAACTATGATCTTTATTATGATTGAATTCACTAAATACTAAGTTCCATACTTCAAGATAGCGTTCATTTTCTCCACCTGGATACATTTCTTCTGCCGGAt                                                                                                                         <  1:219422/141‑1 (MQ=255)                gCCCCATGCCAGTATCAATATTTTTATTAGGTAATGGTGTGTAACTATGATCTTTATTATGATTGAATTCACTAAATACTAAGTTCCATACTTCAAGATAGCGTTCATTTTCTCCACCTGGATACATTTCTTCTGCCGGAt                                                                                                                         <  1:24014/141‑1 (MQ=255)                  cccATGCCAGTATCAATATTTTTATTAGGTAATGGTGTGTAACTATGATCTTTATTATGATTGAATTCACTAAATACTAAGTTCCATACTTCAAGATAGCGTTCATTTTCTCCACCTGGATACATTTCTTCTGCCGGATCg                                                                                                                       >  2:293475/1‑141 (MQ=255)                              tctatatTTTTATTAGGTAAGGGGGGGTAACTATGATTTTTATTATGATTGAATTCACTAAATACTAAGTTCCATACTTCAAGATAGCGTTCATTTTCTCCACCTGGATACATTTCTTCTGCCGGATCGTCTTGTCCatat                                                                                                           <  2:61877/138‑1 (MQ=255)                                    tttttATTAGGTAATGGTGTGTAACTATGATCTTTATTATGATTGAATTCACTAAATACTAAGTTCCATACTTCAAGATAGCGTTCATTTTCTCCACCTGGATACATTTCTTCTGCCGGATCGTCTTGTCCATATGCTtct                                                                                                     >  2:185762/1‑141 (MQ=255)                                                  tggtggGTAACTATGATCTTTATTATGATTGAATTCACTAAATACTAAGGTCCATACTTCAAGATAGCGTTCATTTTCTCCACCTGGATACATTTCTTCTGCCGGATCGTCTTGTCCATATGCTTCTCCGCGATCATAGaa                                                                                       <  2:20836/141‑1 (MQ=255)                                                  tGGTGTGTAACTATGATCTTTATTATGATTGAATTCACTAAATACTAAGTTCCATTCTTCAAGATAGCTTTCATTTTCTCCACCTGGATACATTTCTTCTGCCGGATCGTCTTGTCCATATGCTTCTCCGCGATCATAGaa                                                                                       <  2:66104/141‑1 (MQ=255)                                                     tgtgtAACTATGATCTTTATTATGATTGAATTCACTAAATACTAAGTTCCATACTTCAAGATAGCGTTCATTTTCTCCACCTGTATACATTTCTTCTGCCGGATCGTCTTGTCCATATGCTTCTCCGCGATCATAGAAAAt                                                                                    >  1:343457/1‑141 (MQ=255)                                                     tgtgtAACTATGATCTTTATTATGATTGAATTCACTAAATACTAAGTTCCATACTTCAAGATAGCGTTCATTTTCTCCACCTGTATACATTTCTTCTGCCGGATCGTCTTGTCCATATGCTTCTCCGCGATCATAGAAAAt                                                                                    >  1:361941/1‑141 (MQ=255)                                                                    tttATGATGATTGAATTCACGTAATACTAAGTTCCATACTTCAAGCTAGCGTTCATTTTCTCCACCTGGATACATTTCTTCTGCCGGATCGTCTTGTCCATATGCTTCTCCGCGATCATAGAAAATCTCAGTGTTCGGTcc                                                                     <  2:193322/141‑1 (MQ=255)                                                                         tatGATTGAATTCACTAAATACTAAGTTCCATACTTCAAGATAGCGTTCATTTTCTCCACCTGGATACATTTCTTCTGCCGGATCGTCTTGTCCATATGCTTCTCCGCGATCATAGAAAATCTCAGTGTTCGGTCCTGAAg                                                                >  2:312741/1‑141 (MQ=255)                                                                          atGATTGAATTCACTAAATACTAAGTTCCATACTTCAAGATAGCGTTCATTTTCTCCACCTGGATACATTTCTTCTGCCGGATCGTCTTGTCCATATGCTTCTCCGCGATCATAGAAAATCTCAGTGTTCGGTCCTGAAgg                                                               <  2:73552/141‑1 (MQ=255)                                                                           agATTGAATTCACTAACTACTAAGTTCCATACTTCAAGATAGCGTTCATTTTCTCCACCTGGATACATTTCTTCTGCCGGATCGTCTTGTCCATATGCTTCTCCGCGATCATAGAAAATCTCAGTGTTCGGTCCTGAAGGc                                                              <  1:8434/140‑1 (MQ=255)                                                                                    tCACTAAATACTAAGTTCCATACTTCAAGATAGCGGTCATTTTCTCCACCTGGATACATTTCTTCTGCCGGATCGTCTTGTCCATATGCTTCTCCGCGCTCATAGAAAATCTCAGTGTTCGGTCCTGAAGGCCCTTCACCa                                                     >  2:66197/1‑141 (MQ=255)                                                                                      aCTAAATACTAAGTTCCATACTTCAAGATAGCGTTCATTTTCTCCACCTGGATACATTTCTTCTGCCGGATCGTCTTGTCCATATGCTTCTCCGCGATCATAGAAAATCTCAGTGTTCGGTCCTGAAGGCCCTTCACCAat                                                   <  1:382213/141‑1 (MQ=255)                                                                                        tAAATACTAAGTTCCATACTTCAAGATAGCGTTCATTTTCTCCACCTGGATACATTTCTTCTGCCGGATCGTCTTGTCCATATGCTTCTCCGCGATCATAGAAAATCTCAGTGTTCGGTCCTGAAGGCCCTTCACCAatat                                                 >  2:82564/1‑141 (MQ=255)                                                                                         aaaTACTAAGTTCCATACTTCAAGATAGCGTTCATTTTCTCCACCTGGATACATTTCTTCTGCCGGATCGTCTTGTCCATATGCTTCTCCGCGATCATAGAAAATCTCAGTGTTCGGTCCTGAAGGCCCTTCACCAATATc                                                <  1:381497/141‑1 (MQ=255)                                                                                         aaaCACTAAGTTCCATACTTCAAGATAGCGTTCATTTTCTCCACCTGGATACATTTCTTCTGCCGGATCGTCTTGTCCATATGCTTCTCCGCGATCATAGAAAATCTCAGTGTTCGGTCCTGAAGGCCCTTCACCAATATc                                                <  1:381451/141‑1 (MQ=255)                                                                                               tAAGTTCCATACTTCAAGATAGCGTTCATTTTCTCCACCTGGATACATTTCTTCTGCCGGATCGTCTTGTCCATATGCTTCTCCGCGATCATAGAAAATCTCAGTGTTCGGTCCTGAAGGCCCTTCACCAATATCCCAGaa                                          >  1:101003/1‑141 (MQ=255)                                                                                                          cTTCAAGATAGCGTTCATTTTCTCCACCTGGATACGTTTCTTCTGCCGGATCGTCTTGTCCCTATGCTTCTCCGCGATCATAGAAAATCTCAGTGTTCGGTCCTGAAGGCCCTTCACCAATATCCCAGAAGTTACCTTCaa                               >  2:221077/1‑141 (MQ=255)                                                                                                           ttCAAGATAGCGTTCATTTTCTCCACCTGTATACATTTCTTCTGCCGGATCGTCTTGTCCATATGCTTCTCCGCGATCATAGAAAATCTCAGTGTTCGGTCCTGAAGGCCCTTCACCAATATCCCAGAAGTTACCTTCAAt                              <  2:343457/141‑1 (MQ=255)                                                                                                           ttCAAGATAGCGTTCATTTTCTCCACCTGTATACATTTCTTCTGCCGGATCGTCTTGTCCATATGCTTCTCCGCGATCATAGAAAATCTCAGTGTTCGGTCCTGAAGGCCCTTCACCAATATCCCAGAAGTTACCTTCAAt                              <  2:361941/141‑1 (MQ=255)                                                                                                            tCAAGATAGCGTTCATTTTCTCCACCTGGATACATTTCTTCTGCCGGATCGTCTTGTCCATATGCTTCTCCGCGATCATAGAAAATCTCAGTGTTCGGTCCTGAAGGCCCTTCACCAATATCCCAGAAGTTACCTTCAATg                             >  1:110403/1‑141 (MQ=255)                                                                                                            tCAAGATAGCGTTCATTTTCACCACCTGGATACATTTCTTCTGCCGGATCGTCTTGTCCATATGCTTCTCCGCGGTCATAGAAAATCTCAGTGTTCGGTCCTCAGGGCCCTTCAGCAATATCCCAGAAGTTACCTTCAATg                             >  1:240209/1‑141 (MQ=255)                                                                                                                      gtccATTTTCTCCACCTGGATACATTTCTTCTGCCGGATCGTCTTGTCCATATGCTCCTCCGCGATCCTAGAAAATCTCACTGTTCTTTCCGGAAGGCACTATGCCGATAGCCCAGGAGTTACCTTCAATGAGAATAATAc                   <  1:289495/138‑1 (MQ=255)                                                                                                                      gTTCATTTTCTCCACCTGGATACATTTCTTCTGCCGGATCGTCTTGTCCATATGCTTCTCCGCGATCATAGAAAATCTCAGTGTTCGGTCCTGAAGGCCCTTCACCAATATCCCAGAAGTTACCTTCAATGCGAATAATAc                   <  1:205874/141‑1 (MQ=255)                                                                                                                            tttCTCCACCTGGATACATTTCTTCTGCCGGATCGTCTTGTCCATATGCTTCTCCGCGATCATAGAAAATCTCAGTGTTCGGTCCTTAAGGCCCTTCACCAATATCCCAGAAGTTACCTTCAATGCGAATAATACGACttt             >  2:245932/1‑141 (MQ=255)                                                                                                                            tttCTCCACCTGGATACATTTCTTCTGCCGGATCGTCTTGTCCATATGCTTCTCCGCGATCATAGAAAATCTCAGTGTTCGGTCCTGAGGGCCCTTCACCAATATCCCAGAAGTTACCTTCAATGCGAATAATTCGACttt             >  2:433/1‑141 (MQ=255)                                                                                                                               ctcCACCTGGATACATTTCTTCTGCCGGATCGTCTTGTCCATATGCTTCTCCGCGATCATAGAAAATCTCAGTGTTCGGTCCTGAAGGCCCTTCACCAATATCCCAGAAGTTACCTTCAATGCGAATAATACGACTatctt          >  1:153171/1‑141 (MQ=255)                                                                                                                               ctcCACCTGGATACATTTCTTCTGCCGGATCGTCTTGTCCATATGCTTCTCCGCGATCATAGAAAATCTCAGTGTTCGGTCCTGAAGGCCCTTCACCAATATCCCAGAAGTTACCTTCAATGCGAAAAATACGACTttctt          >  1:391525/1‑141 (MQ=255)                                                                                                                                       ggATACATTTCTTCTGCCGGATCGTCTTGTCCATATGCTTCTCCGCGATCATAGAAAATCTCAGTGTTCGGTCCTGAAGGCCCTTCACCAATATCCCAGAAGTTACCTTCAATGCGAATAATACGACTTTCTTCAAGCCCa  >  1:272679/1‑141 (MQ=255)                                                                                                                                        |                                                                                                                                            AGGCCATACGCTCAAGCCCCATGCCAGTATCAATATTTTTATTAGGTAATGGTGTGTAACTATGATCTTTATTATGATTGAATTCACTAAATACTAAGTTCCATACTTCAAGATAGCGTTCATTTTCTCCACCTGGATACATTTCTTCTGCCGGATCGTCTTGTCCATATGCTTCTCCGCGATCATAGAAAATCTCAGTGTTCGGTCCTGAAGGCCCTTCACCAATATCCCAGAAGTTACCTTCAATGCGAATAATACGACTTTCTTCAAGCCCA  >  USA300TCH1516_ALE/1724571‑1724845

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑