Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	728,467	T→C	I1143I (ATT→ATC)	rhsC →	rhs element protein RhsC

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	728,467	0	T	C	100.0%	118.4 / NA	35	I1143I (ATT→ATC)	rhsC	rhs element protein RhsC
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (20/15);  total (20/15)

AAAGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATTCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGAAT  >  NZ_CP009273/728379‑728546                                                                                         |                                                                                aaaGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCa                                                                               <  2:73226/91‑1 (MQ=37)   aGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCAcc                                                                             <  1:511637/91‑1 (MQ=255)                       gTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATcgc                                                         <  1:204804/91‑1 (MQ=37)                       gTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATcgc                                                         <  2:464858/91‑1 (MQ=37)                       gTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATcgc                                                         >  2:738964/1‑91 (MQ=255)                       gTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATcgc                                                         >  1:486016/1‑91 (MQ=255)                       gTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATcgc                                                         >  2:755148/1‑91 (MQ=255)                       gTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATcgc                                                         <  1:349742/91‑1 (MQ=37)                       gTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATcgc                                                         >  2:794710/1‑91 (MQ=255)                            gCCTAACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCt                                                    <  2:324651/91‑1 (MQ=255)                             ccTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCACCTCGGCCTg                                                   <  1:809173/91‑1 (MQ=255)                                  cGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCt                                              <  2:721348/91‑1 (MQ=37)                                    gTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTgg                                            <  1:45025/91‑1 (MQ=37)                                      ggCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGcc                                          >  2:783864/1‑91 (MQ=255)                                       gcgcAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGccc                                         <  2:380859/91‑1 (MQ=25)                                            gATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATc                                    >  1:353310/1‑91 (MQ=21)                                                 aaaGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAACCCTCCTGTCCCACTGCGCCCATCGCCGCCTGCCGCTGGCCCTTATCAGCAc                               <  2:441641/91‑1 (MQ=11)                                                   aGCCAGATGGCCCCGGTATACACGCCGGCGCGAAAAATCCCCCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACgg                             <  2:586258/91‑1 (MQ=255)                                                     ccAGATGGACCGGGTATACACGCCGGCGCGAAAAATCCGCCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGaa                           <  2:348459/91‑1 (MQ=255)                                                     ccAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGaa                           <  1:413722/91‑1 (MQ=21)                                                      cAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAg                          >  2:698161/1‑91 (MQ=21)                                                              cccGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGacaaca                  >  2:226772/1‑91 (MQ=18)                                                              cccGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGacaaca                  >  1:828823/1‑91 (MQ=18)                                                                         cGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGc       <  2:408760/91‑1 (MQ=255)                                                                         cGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGc       <  1:348857/91‑1 (MQ=255)                                                                          gCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCa      >  2:780384/1‑91 (MQ=255)                                                                          gCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGCCCTGCCCCTCCCCCTTACCAGCACGGAAGGGCCAACAGCGTGGTAcccc      >  2:615409/1‑88 (MQ=11)                                                                           ccGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAg     >  1:626675/1‑91 (MQ=255)                                                                           ccGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAg     >  1:489718/1‑91 (MQ=255)                                                                            cGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGa    >  1:331789/1‑91 (MQ=255)                                                                            cGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGa    >  2:775519/1‑91 (MQ=255)                                                                            cGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGa    >  1:649259/1‑91 (MQ=255)                                                                            cGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGa    >  2:148855/1‑91 (MQ=255)                                                                            cGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGa    >  2:382663/1‑91 (MQ=255)                                                                              gcgcGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGAAt  >  2:513838/1‑91 (MQ=255)                                                                              gcgcGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGAAt  >  1:867985/1‑91 (MQ=255)                                                                                         |                                                                                AAAGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATTCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGAAT  >  NZ_CP009273/728379‑728546

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑