Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,619,272	T→C	R27R (CGT→CGC)	rhsB →	rhs element protein RhsB

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,619,272	0	T	C	100.0%	73.5 / NA	27	R27R (CGT→CGC)	rhsB	rhs element protein RhsB
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (12/15);  total (12/15)

CTTTTTCGTATGAAGATACTGTCATTAAAATAATAGAAAAGGATTTTACGATGAGCGGAAAACCGGCGGCGCGTCAGGGTGACATGACGCAGTATGGCGGTAGCATTGTTCAGGGTTCAGCCGGGGTACGTATTGGTGCCCCCACCGGCGTGGCCTGTTCGGTGTGCCCCGGCGGAGTGACGTCCGGCCATCCGGTCAATCCCCTGCT  >  NC_000913/3619142‑3619349                                                                                                                                   |                                                                              cTTTTTCGTATGAAGATACTGTCATTAAAATAATAGAAAAGGATTTTACGATGAGCGGAAAACCGGCGGCGCGTCAGGGTGACATGACGCAGTATGGCGGTAGCATTTTTTAGGGGTTAGCCGGGGGACGCATTGGTGcc                                                                      >  2:469703/1‑140 (MQ=25)     ttCGTATGAAGATACTGTCATTAAAATAATAGAAAAGGATTTTACGATGAGCGGAAAACCGGCGGCGCGTCAGGGTGACATGACGCAGTATGGCGGTAGCATTGTTCAGGGTTCAGCCGGGGTACGCATTGGTGCCCCCa                                                                  <  1:295273/140‑1 (MQ=255)     ttCGTATGAAGATACTGTCATTAAAATAATAGAAAAGGATTTTACGATGAGCGGAAAACCGGCGGCGCGTCAGGGTGACATGACGCAGTATGGCGGTAGCATTGTTCAGGGTTCAGCCGGGGTACGCATTGGTGCCCCCa                                                                  <  1:351729/140‑1 (MQ=255)     ttCGTATGAAGATACTGTCATTAAAATAATAGAAAAGGATTTTACGATGAGCGGAAAACCGGCGGCGCGTCAGGGTGACATGACGCAGTATGGCGGTAGCATTGTTCAGGGTTCAGCCGGGGTACGCATTGGTGCCCCCa                                                                  <  1:103173/140‑1 (MQ=255)            gAAGATACTGTCATTAAAATAATAGAAAAGGATTTTACGATGAGCGGAAAACCGGCGGCGCGTCAGGGTGACATGACGCAGTATGGCGGTAGCATTGTTTAGGGTTGAGGCGGGGGACGCATTTGGGCCCCCACCcgcgg                                                           >  2:956151/1‑139 (MQ=21)                   cTGTCATTAAAATAATAGAAAAGGATTTTACGATGAGCGGAAAACCGGCGGCGCGTCAGGGTGACATGACGCAGTATGGCGGTAGCATTGTTCAGGGTTCAGCCGGGGTACGCATTGGTGCCCCCACCGGCGTGGCCTGt                                                    <  2:74362/140‑1 (MQ=255)                   cTGTCATTAAAATAATAGAAAAGGATTTTACGATGAGCGGAAAACCGGCGGCGCGTCAGGGTGACATGACGCAGTATGGCGGTAGCATTGTTCAGGGTTCAGCCGGGGTACGCATTGGTGCCCCCACCGGCGTGGCCTGt                                                    >  1:944243/1‑140 (MQ=255)                    tGTCATTAAAATAATAGAAAAGGATTTTACGATGAGCGGAAAACCGGCGGCGCGTCAGGGTGACATGACGCAGTATGGCGGTAGCATTTTTCAAGGTTCAGCCGGGGGACGCATTGGTGCCCCCACCCGCGTGGGCCGtt                                                   >  2:887390/1‑140 (MQ=18)                      tCATTAAAATAATAGAAAAGGATTTTACGATGAGCGGAAAACCGGCGGCGCGTCAGGGTGACATGACGCAGTATGGCGGTAGCATTGTTTAGGGGTCAGCCGGGGGACGCATTGGTGCCCCCACCGGCGGGGCCTGTTCg                                                 >  2:435654/1‑140 (MQ=18)                       cATTAAAATAATAGAAAAGGATTTTACGATGAGCGGAAAACCGGCGGCGCGTCAGGGTGACATGACGCAGTATGGCGGTAGCATTGTTCAGGGTTCAGCCGGGGGACGCATTGGTGCCCCCACCGGCGTGGCCTGTTCgg                                                >  1:654013/1‑140 (MQ=255)                        aTTAAAATAATAGAAAAGGATTTTACGATGAGCGGAAAACCGGCGGCGCGTCAGGGTGACATGACGCAGTATGGCGGTAGCATTGTTCAGGGTTCAGCCGGGGTACGCATTGGTGCCCCCCCCGGCGTGGCCTGTTCGgt                                               >  2:394611/1‑140 (MQ=255)                         ttAAAATAATAGAAAAGGATTTTACGATGAGCGGAAAACCGGCGGCGCGTCAGGGTGACATGACGCAGTATGGCGGTAGCATTGTTCAGGGTTCAGCCGGGGTACGCATTGGTGCCCCCACCGGCGTGGCCTGTTCGgtg                                              <  1:664066/140‑1 (MQ=255)                          tAAAATAATAGAAAAGGATTTTACGATGAGCGGAAAACCGGCGGCGCGTCAGGGTGACATGACGCAGTATGGCGGTAGCATTGTTCAGGGTTCAGCCGGGGTACGCATTGGTGCCCCCACCGGCGTGGCCTGTTCGgtgt                                             >  2:822919/1‑140 (MQ=255)                          tAAAATAATAGAAAAGGATTTTACGATGAGCGGAAAACCGGCGGCGCGTCAGGGTGACATGACGCAGTATGGCGGTAACATTGTTTCGGGGTCAGCCGGGGGACGCCTTGGTGCCCCCCCCCGCGTGGGCCGTTCggggg                                             >  2:236024/1‑137 (MQ=17)                              ataataGAAAAGGATTTTACGATGAGCGGAAAACCGGCGGCGCGTCAGGGTGACATGACGCAGTATGGCGGTAGCATTGTTCAGGGTTCAGCCGGGGTACGCATTGGTGCCCCCACCGGCGTgg                                                         >  1:516616/1‑124 (MQ=255)                              ataataGAAAAGGATTTTACGATGAGCGGAAAACCGGCGGCGCGTCAGGGTGACATGACGCAGTATGGCGGTAGCATTGTTCAGGGTTCAGCCGGGGTACGCATTGGTGCCCCCACCGGCGTgg                                                         <  2:516616/124‑1 (MQ=255)                              ataataGAAAAGGATTTTACGATGAGCGGAAAACCGGCGGCGCGTCAGGGTGACATGACGCAGTATGGCGGTAGCATTGTTCAGGGTTCAGCCGGGGTACGCATTGGTGCCCCCACCGGCGTGGCCTGTTCGGTGTGccc                                         <  1:236024/140‑1 (MQ=255)                                aataGAAAAGGATTTTACGATGAGCGGAAAACCGGCGGCGCGTCAGGGTGACATGACGCAGTATGGCGGTAGCATTGTTCAGGGTTCAGCCGGGGGACGCATTGGTGCCCCCACCGGCGTGGCCTGTTCGGGGTGccccc                                       >  2:880478/1‑139 (MQ=255)                                  taGAAAAGGATTTTACGATGAGCGGAAAACCGGCGGCGCGTCAGGGTGACATGACGCAGTATGGCGGTAGCATTGTTCAGGGTTCAGCCGGGGTACGCATTGGTGCCCCCACCGGCGTGGCCTGTTCGGTGTGCCCcggc                                     <  1:435654/140‑1 (MQ=255)                                      aaaGGATTTTACGATGAGCGGAAAACCGGCGGCGCGTCAGGGTGACATGACGCAGTATGGCGGTAGCATTGTTCAGGGTTCAGCCGGGGTACGCATTGGTGCCCCCACCGGCGTGGCCTGTTCGGTGTGCCCCGGCGGAg                                 >  1:909035/1‑140 (MQ=255)                                               tACGATGAGCGGAAAACCGGCGGCGCGTCAGGGTGACATGACGCAGTATGGCGGTAGCATTGTTCAGGGTTCAGCCGGGGGACGCATTGGTGCCCCCACCGGCGTGGCCTGTTCGGGGTGCCCCCGCGGGGTGACGTccc                        >  2:505973/1‑139 (MQ=11)                                                    tGAGCGGAAAACCGGCGGCGCGTCAGGGTGACATGACGCAGTATGGCGGTAGCATTGTTCAGGGTTCAGCCGGGGTACGCATTGGTGCCCCCACCGGCGTGGCCTGTTCGGTGTGCCCCGGCGGAGTGACGTCCGGCCAt                   >  2:497650/1‑140 (MQ=25)                                                          gAAAACCGGCGGCGCGTCAGGGTGACATGACGCAGTATGGCGGTAGCATTGTTCAGGGTTCAGCCGGGGTACGCATTGGTGCCCCCACCGGCGTGGCCTGTTCGGTGTGCCCCGGCGGAGTGACGTCCGGCCATCCGGTc             <  2:944243/140‑1 (MQ=21)                                                           aaaaCCGGCGGCGCGTCAGGGTGACATGACGCAGTATGGCGGTAGCATTGTTCAGGGTTCAGCCGGGGTACGCATTGGTGCCCCCACCGGCGTGGCCTGTTCGGTGTGCCCCGGCGGAGTGACGTCCGGCCATCCGGTCa            <  2:264608/140‑1 (MQ=21)                                                           aaaaCCGGCGGCGCGTCAGGGTGACATGACGCAGTATGGCGGTAGCATTGTTCAGGGTTCAGCCGGGGTACGCATTGGTGCCCCCACCGGCGTGGCCTGTTCGGTGTGCCCCGGCGGAGTGACGTCCGGCCATCCGGTCa            <  1:394611/140‑1 (MQ=21)                                                           aaaaCCGGCGGCGCGTCAGGGTGACATGACGCAGTATGGCGGTAGCATTGTTCAGGGTTCAGCCGGGGTACGCATTGGTGCCCCCACCGGCGTGGCCTGTTCGGTGTGCCCCGGCGGAGTGACGTCCGGCCATCCGGTCa            <  2:909035/140‑1 (MQ=21)                                                                cggcggCGCGTCAGGGTGACATGACGCAGTATGGCGGTAGCATTGTTCAGGGTTCAGCCGGGGGACGCCTTGGTGCCCCCCCCCGCGTGGGCTGTTCGGTGTGCCCCCGCGGAGGGACGGCCGGCCCTCCCGGCAATccc       >  2:5933/1‑140 (MQ=11)                                                                  gcggcgCGTCAGGGTGACATGACGCAGTATGGCGGTAGCATTGTTCAGGGGTCAGCCGGGGTACGCATTGGTGCCCCCACCGGCGTGGCCTGTTCGGTGTGCCCCGGCGGAGTGACGTCCGGCCATCCGGTCAATCCCCt     >  2:154722/1‑140 (MQ=21)                                                                     gcgcGTCAGGGTGACATGACGCAGTATGGCGGTAGCATTGTTCAGGGTTCAGCCGGGGTACGCATTGGTGCCCCCACCGGCGTGGCCTGTTCGGTGTGCCCCGGCGGAGTGACGTCCGGCCATCCGGTCAATCCCCTGCt  <  1:880478/140‑1 (MQ=17)                                                                     gcgcGTCAGGGTGACATGACGCAGTATGGCGGTAGCATTGTTCAGGGTTCAGCCGGGGTACGCATTGGTGCCCCCACCGGCGTGGCCTGTTCGGTGTGCCCCGGCGGAGTGACGTCCGGCCATCCGGTCAATCCCCTGCt  <  1:822919/140‑1 (MQ=17)                                                                     gcgcGTCAGGGTGACATGACGCAGTATGGCGGTAGCATTGTTCAGGGTTCAGCCGGGGTACGCATTGGTGCCCCCACCGGCGTGGCCTGTTCGGTGTGCCCCGGCGGAGTGACGTCCGGCCATCCGGTCAATCCCCTGCt  <  1:956151/140‑1 (MQ=17)                                                                                                                                   |                                                                              CTTTTTCGTATGAAGATACTGTCATTAAAATAATAGAAAAGGATTTTACGATGAGCGGAAAACCGGCGGCGCGTCAGGGTGACATGACGCAGTATGGCGGTAGCATTGTTCAGGGTTCAGCCGGGGTACGTATTGGTGCCCCCACCGGCGTGGCCTGTTCGGTGTGCCCCGGCGGAGTGACGTCCGGCCATCCGGTCAATCCCCTGCT  >  NC_000913/3619142‑3619349

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑