Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,864,675	G→T	13.7%	G16V (GGT→GTT)	cspLA →	Cold shock‑like protein CspLA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,864,675	0	G	T	13.7%	73.5 / 2.8	29	G16V (GGT→GTT)	cspLA	Cold shock‑like protein CspLA
Reads supporting (aligned to +/- strand):  ref base G (17/8);  new base T (2/2);  total (19/10)
Fisher's exact test for biased strand distribution p-value = 5.92e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.89e-01

ATTGTAGTGTATTTGTTTAGAATATCCTCTTTTTTAGTTATGAATTTGTTACAAATATTAAGTGCAAAAGCACACGGAGGTTTTCTATATGAATAACGGTACAGTAAAATGGTTTAACGCAGAAAAAGGTTTTGGTTTCATCGAACAAGAAAATGGCGGAGACGTATTCGTACATTTCTCAGGTATCGCTAGCGATGGCTACAAAACTTTAGAAGAAGGTCAAAAAGTTACTTTCGAAATCACTGAAGGTCAACGTGGAGACCAAGCAG  >  USA300TCH1516_ALE/2864541‑2864809                                                                                                                                       |                                                                                                                                       aTTGTAGTGTATTTGTTTAGAATATCCTCTTTTTTAGTTATGAATTTGTTACAAATATTAAGTGCAAAAGCACACGGAGGTTTTCTATATGAATAACGGTACAGTAAAATGGTTTAACGCAGAAAAAGGTTTTGGTTTCa                                                                                                                                   >  1:240073/1‑140 (MQ=255)   tGTAGTGTATTTGTTTAGAATATCCTTTTTTTTAGTTATGAATTTGTTACAAATATTAAGTGCAAAAGCACACGGAGGTTTTCTATATGAATAACGGTACAGTAAAATGGTTTAACGCAGAAAAAGGTTTTGTTTTCATc                                                                                                                                 <  2:75760/140‑1 (MQ=255)               gcttAGAATATCCTCTTTTTTAGTTATGAATTTGTTACAAATATTCAGTGCAAAATCACACGGAGGTTTTCTATATGAATAACTGTACAGTAAAATGGTTTAACGCAGAAAAAGGTTTTGGTTTCATCGAACAAGAAAAt                                                                                                                     <  2:324093/138‑1 (MQ=255)               gTTTAGAATATCCTCTTTTTTAGTTATGAATTTGTTACAAATATTAAGTGCAAAAGCACACGGAGGTTTTCTATATGAATAACGGTACAGTAAAATGGTTTAACGCAGAAAAAGGTTTTGGTTTCATCGAACAAGAAAAt                                                                                                                     <  1:220078/140‑1 (MQ=255)                                    aatagtGAATTTGTTAAAAATATTAATTGCAAAAGCACACGGAGGTTTTCTATATGAATAACGGTACAGTAAAATGGTTTAACGCAGAAAAAGGTTTTGGTTTCATCGAACAAGAAAATGGCGGAGACGTATTCGTACAt                                                                                                <  1:132042/135‑1 (MQ=255)                                     gTTATGAATTTGTTACAAATATTAAGTGCAAAAGCACACGGAGGTTTTCTATATGAATAACGGTACAGTAAAATGGTTTAACGCAGAAAAAGGTTTTGGTTTCATCGAACAAGAAAATGGCGGAGACGTATTCGTACAtt                                                                                               >  2:237553/1‑140 (MQ=255)                                               tGTTACAAATATTAAGTGCAAAAGCAGACGGAGGTTTTCTATATGAATAACGGTAGAGTAAGATGGTTTAACGCAGAAAAAGGAATTGGAATAATCGAACAAGAAAATGGCGGAAAAGTATTCGTACAGTTCTCAGGGAt                                                                                     >  2:226644/1‑140 (MQ=255)                                                    cAAATATTAAGTGCAAAAGCACACGGAGGTTTTCTATATGAATAACGGTACAGTAAAATGGTTTAACGCAGAAAAAGGTTTTGGTTTCATCGAACAAGAAAATAGCGGAGACGTATTCGTACATTTCTCAGGTATCGCTa                                                                                >  1:2996/1‑140 (MQ=255)                                                      aaTATTAAGTGCAAAAGCACACGGAGGTTTTCTATATGAATAACGGTACAGTAAAATGGTTTAACGCAGAAAAAGGTTTTGGTTTCATCGAACAAGAAAATGGCGGAGACGTATTCGTACATTTCTCAGGTATCGCTAGc                                                                              >  1:101798/1‑140 (MQ=255)                                                             aGTGCAAAAGCACACGGAGTTTTTCTATATGAATAACGGTACAGTAAAATGGTTTAACGCAGAAAAAGGTTTTGGTTTCATCGAACAAGAAAATGGCGGAGACGTATTCGTACATTTCTCAGGTATCGCTAGCGATGGCt                                                                       <  2:240073/140‑1 (MQ=255)                                                             aGTGCAAAAGCACACGGAGGTTTTCTATATGAATAACGGTACAGTAAAATGGTTTAACGCAGAAAAAGGTTTTGGTTTCATCGAACAAGAAAATGGCGGAGACGTATTCGTACATTTCTCAGGTATCGCTAGCGATGGCt                                                                       <  2:47863/140‑1 (MQ=255)                                                              gTGCAAAAGCACACGGAGGTTTTCTATATGAATAACGGTACAGTAAAATGGTTTAACGCAGAAAAAGGTTTTGGTTTCATCGAACAAGAAAATGGCGGAGACGTATTCGTACATTTCTCAGGTATCACTAGCGATGGCTa                                                                      >  1:341115/1‑140 (MQ=255)                                                                      gCACACGGAGGTTTTCTATATGAATAACGGTACAGTAAAATGGTTTAACGCAGAAAAAGGTTTTGGTTTCATCGAACAAGAAAATGGCGGAGACGTATTCGTACATTTCTCAGGTATCGCTAGCGATGGCTACAAAACtt                                                              <  2:113332/140‑1 (MQ=255)                                                                       cacaCGGAGGTTTTCTATATGAATACGGGCACAGTAAAATGGTTTAACGCAGAAAAAGGTTTTGGTTTCATCGAACAAGAAAATGGCGGAGACGTATTCGTACATTTCTCAGGTATCGCTAGCGATGGCTACAAAACttt                                                             >  1:353700/1‑140 (MQ=255)                                                                           cGGAGGTTTTCTATATGCCGTCCGAGACAGTAAAATGGTTTAACGCAGAAAAAGGTTTTGTTTTCATCGAACAAGAAAATGGCGGAAACGTATTCGTACATTTCCCAGGTATCGCTAGCGATGGCTACAAAACTTTagaa                                                         >  2:164140/1‑140 (MQ=255)                                                                           cGGAGGTTTTCTATATGAATAACGGTACAGTAAAATGGTTTAACGCAGAAAAAGGTTTTGGTTTCATCGAACAAGAAAATGGCGGAGACGTATTCGTACATTTATCAGGTATCGCTAGCGATGGCTACAAAACTTTagaa                                                         >  2:282131/1‑140 (MQ=255)                                                                           cGGAGGTTTTCTATATGAATAACGGTACAGTAAAATGGTTTAACGCAGAAAAAGG‑TTTGGTTTCATCGAACAAGAAAATGGCGGAGACGTATTCGTACATTTCTCAGGTATCGCTAGCGATGGCTACAAAACTTTagaag                                                        >  2:318282/1‑140 (MQ=255)                                                                             gAGGTTTTCTATATGAATAACGGTACAGTAAAATGGTTTAACGCAGAAAAAGGTTTTGGTTTCATCGAACAAGAAAATGGCGGAAACGTATTCGTACATTTCTCAGGTATCACTAGCGAAGGCTACAAAAATTTaaaaga                                                       >  1:137448/1‑140 (MQ=25)                                                                               ggTTTTCTATATGAATAACGGTACAGTAAAATGGTTTAACGCAGAAAAAGGTTTTGGTTTCATCGAACAAGAAAATGGCGGAGAAGTATTCGTACATTTCTCAGGTATCGATAGCAATGGCTACAAAACTTTAGaagaag                                                     >  1:166943/1‑140 (MQ=255)                                                                                                    tACAGTAAAATGGTTTAACGCAGAAAAATGTTTTGGTTTCATCGAACAAGAAAATGGCGGAGACGTATTCGTACATTTCTCAGGTATCGCTAGCGATGGCTACAAAACTTTAGAAGAAGGTCAAAAAGTTACTTTCGaaa                                <  2:130249/140‑1 (MQ=255)                                                                                                    tACAGTAAAATGGTTTAACGCAGAAAAAGGTTTTGTTTTCATCGAACAAGAAAATGGCGGAGACGTATTCGTACATTTCTCAGGTATCGCTAGCGATGGCTACAAAACTTTAGAAGAAGGTCAAAAAGTTACTTTCGaaa                                >  2:179525/1‑140 (MQ=255)                                                                                                       aGTAAAATGGTTTAACGCAGAAAAAGGTTTTGGTTTCATCGAACAAGAAAATGGCGGAGACGTATTCGTACATTTCTCAGGTATCGCTAGCGATGGCTACAAAACTTTAGAGGAAGGTCAAAAATTTGTTTTCGAAAtaa                             >  2:101250/1‑138 (MQ=25)                                                                                                        gTAAAATGGTTTAACGCAGAAAAAGGTTTTGGTTTCATCGAACAAGAAAATGGCGGAGGCGTATTCGTACATTTCTCAGGTATCGCTAGCGATGGCTACAAAACTTTAGAAGAAGGTCAAAAAGTTACTTTCGAAATCAc                            >  1:215006/1‑140 (MQ=255)                                                                                                               ggTTTAACGCAGAAAAAGGTTTTGGTTTCATCGAACAAGAAAATGGCGGAGACGTATTCGTACATTTCTCAGGTATCGCTAGCGATGGCTACAAAACTTTAGAAGAAGGTCAAAAAGTTACTTTCGAAATCACTGAAGGt                     <  1:307048/140‑1 (MQ=255)                                                                                                                  ttAACGCAGAAAAAGGTTTTGGTTTCATCGAACAAGAAAATGGCGGAGACGTATTCGTACATTTCTCAGGTATCGCTAGCGATGGCTACAAAACTTTAGAAGAAGGTCAAAAAGTTACTTTCGAAATCAATGAAGGTCaa                  >  1:30205/1‑140 (MQ=255)                                                                                                                   tAACTCATAAAAAGGTTTTGTTTTCATCGAACAAGAAAATTGCTTATACTTATTCTTACATTTCTCAGGTATCGCTAGCGATGGCTACAAAACTTTAGAAGAAGGTCAAAAAGTTACTTTCGAAATCACTGAAGGTCAAc                 <  1:276291/140‑1 (MQ=255)                                                                                                                    aaCGCAGAAAAAGGTTTTGGTTTCATCGAACAAGAAAATGGCGGAGACGTATTCGTACATTTCTCAGGTATCGCTAGCGATGGCTACAAAACTTTAGAAGAAGGTCAAAAAGTTACTTTCGAAATCACTGAAGGTCAACg                >  2:275777/1‑140 (MQ=255)                                                                                                                             aaaGGTTTTGGTTTCATCGAACAAGAAAATGGCGGAGACGTATTCGTACATTTCTCAGGTATCGCTAGCGATGGCTACAAAACTTTAGAAGAAGGTCCAAAAGTTACTTTCGAAATCACTGAAGGTCACCGTGGAGACCa       >  2:106834/1‑140 (MQ=255)                                                                                                                                  ttttGGTTTCATCGAACAAGAAAATGGCGGAGACGTATTCGTACATTTCTCAGGTATCGCTAGCGATGGCTACAAAACTTTAGAAGAAGGTCAAAAAGTTACTTTCGAAATCACTGAAGGTCAACGTGGAGAACAAgacg  >  2:39307/1‑137 (MQ=255)                                                                                                                                       |                                                                                                                                       ATTGTAGTGTATTTGTTTAGAATATCCTCTTTTTTAGTTATGAATTTGTTACAAATATTAAGTGCAAAAGCACACGGAGGTTTTCTATATGAATAACGGTACAGTAAAATGGTTTAACGCAGAAAAAGGTTTTGGTTTCATCGAACAAGAAAATGGCGGAGACGTATTCGTACATTTCTCAGGTATCGCTAGCGATGGCTACAAAACTTTAGAAGAAGGTCAAAAAGTTACTTTCGAAATCACTGAAGGTCAACGTGGAGACCAAGCAG  >  USA300TCH1516_ALE/2864541‑2864809

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: ‑