Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	2,502,887	(A)5→6	coding (1411/2106 nt)	USA300HOU_2364 →	AraC transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,502,882	1	.	A	100.0%	98.9 / NA	30	S469* (TCA→TAA)	USA300HOU_2364	AraC transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base A (11/19);  total (11/19)

TCATCTTAAAATTAAAAACAAAAATAAAGAAATTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTC‑AAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATATCATCAACACAATTTGTATATAATAACCTGT  >  CP000730/2502736‑2503010                                                                                                                                                    |                                                                                                                                 tCATCTTAAAATTAAAAACAAAAATAAAGAAATTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTTAAAATTC‑a                                                                                                                                 >  1:84941/1‑148 (MQ=255)        aaaattaaaaACAAAAATAAAGAAATTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTC‑aaaaaact                                                                                                                          <  2:17612/148‑4 (MQ=255)          aattaaaaACAAAAATAAAGAAATTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTC‑aaaaaactgc                                                                                                                        >  2:188087/1‑143 (MQ=255)                 aaCAAAAATAAAGAAATTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACAt                                                                                                                  <  1:244594/148‑1 (MQ=255)                    aaaaaTAAAGAAATTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCtt                                                                                                               <  1:368288/148‑1 (MQ=255)                                aTTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAAc                                                                                                   <  1:273836/148‑1 (MQ=255)                                aTTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTAATCAAACATAAAACAAGTTTATAATGTCATGCAGCGTCTAAAATTCCATTACTACTTTATTTATAAAAAAAAATAAAAAAACTGCAACACAACTTAACACTAAAAAc                                                                                                   <  2:240870/148‑1 (MQ=255)                                    aaTATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAac                                                                                               >  1:249376/1‑148 (MQ=255)                                    aaTATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAac                                                                                               >  2:309489/1‑148 (MQ=255)                                    aaTATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAac                                                                                               >  1:238454/1‑148 (MQ=255)                                                 aGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAAc                                                                                  >  1:386394/1‑148 (MQ=255)                                                    cGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGa                                                                               <  1:49801/148‑1 (MQ=255)                                                    cGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGa                                                                               <  2:263328/148‑1 (MQ=255)                                                      aTGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGaca                                                                             <  1:46049/148‑1 (MQ=255)                                                        ggCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACt                                                                           >  1:248183/1‑148 (MQ=255)                                                           tttttAGAAACTTATTCAAACGTGAAACAAGTTTATAATGACATTCAGCATCTTAAATTCCATTATTACTTTATTAATAAAAAAAAATCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCAt                                                                        <  2:286858/148‑1 (MQ=255)                                                              ttAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCAtttt                                                                     <  2:301221/148‑1 (MQ=255)                                                                   aaCTTATTCACCCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACa                                                                <  1:355651/148‑1 (MQ=255)                                                                   aaCTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACa                                                                <  1:355653/148‑1 (MQ=255)                                                                           cAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGa                                                        <  2:248183/148‑1 (MQ=255)                                                                            aaCCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGaa                                                       <  1:380535/148‑1 (MQ=255)                                                                                 tGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAattta                                                  <  2:347847/148‑1 (MQ=255)                                                                                  ggAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAatttat                                                 <  1:149173/148‑1 (MQ=255)                                                                                     aCAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTAtttt                                              >  2:195533/1‑148 (MQ=255)                                                                                      cAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTa                                             <  2:125307/148‑1 (MQ=255)                                                                                          tttATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGAtt                                         >  1:51289/1‑148 (MQ=255)                                                                                                  gTCATGCAGCGTCTTAAATTCCATTAGTACTTTATTGATAAAAAAAAAACAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGtata                                 <  2:45503/148‑1 (MQ=255)                                                                                                                tAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATATCATCAACACAAtt                   <  2:46386/148‑1 (MQ=255)                                                                                                                tAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATATCATCAACACAAtt                   <  2:109694/148‑1 (MQ=255)                                                                                                                      ccATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATATCATCAACACAATTTGtata             >  2:1077/1‑148 (MQ=255)                                                                                                                          tattaCTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATATCATCAACACAATTTGTATataat         >  2:361432/1‑148 (MQ=255)                                                                                                                          tactaCTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATATCATCAACACAATTTGTATataat         >  2:98863/4‑148 (MQ=255)                                                                                                                                 ttATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATATCATCAACACAATTTGTATATAATAACctgt  >  1:148889/1‑148 (MQ=255)                                                                                                                                                    |                                                                                                                                 TCATCTTAAAATTAAAAACAAAAATAAAGAAATTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTC‑AAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATATCATCAACACAATTTGTATATAATAACCTGT  >  CP000730/2502736‑2503010

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