Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,518,681	A→C	K52T (AAG→ACG)	insA7 →	IS1 family repressor protein InsA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,518,681	0	A	C	100.0%	73.8 / NA	30	K52T (AAG→ACG)	insA7	IS1 family repressor protein InsA
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base C (21/9);  total (21/9)

CTAAAGGATGGGGATTTCGGTAATGCTGCCAACTTACTGATTTAGTGTATGATGGTGATTTTAAGGTGCTTGCGTGGCTTCCATTTCCATCAGATGTCCTTCCTGCTCCGCTACTGAAGGCGTGGTGCGTAACGGCAAAAGCACTGCCGGACATCAGCGCTATCTCTGCTCTCCTTGCCGTAAAACATGGCAACTACAGTTCACTTACACCGCCTCTCAGCCCGGTAAGCACCAGAAAATCATTGATATGGCCATGAATGGCGTCGGATGTCGCGCCAGTGCACGCATTATGGGCGTTGGCCTCAACACGGTTTTACGTCACTTAAAAAACTCAGGCCGCAGTCGGTAACCTCGCGCATACAACCGGGCAGTGATGTGATTGTCTGCGCTGAAATGGACGAACAGTGGGGCTACGTCGGTGCTAAATCACGTCAGCGCTGGCTGTTTTACGCGTATGACAGGATACGGAGG  >  NC_000913/4518454‑4518924                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                                    cTAAAGGATGGGGATTTCGGTAATGCTGCCAACTTACTGATTTAGTGTATGATGGTGATTTTAAGGTGCTTGCGTGGCTTCCATTTCCATCAGATGTCCTTCCTGCTCCGCTACTGAAGGCGTGGTGCGTAACGGCAAAAGCACTGCCGGACATCAGCGCTATCTCTGCTCTCATTGCCGTAAAACATGGCAACTACAGTTCACTTACACCGCCTCTCCGCCCGGAACGCACCCGAAAATAATTGATATgg                                                                                                                                                                                                                              >  2:227277/1‑251 (MQ=255)        atgggactttCGGTAATGCTGACAACTTACTGATCTAGCGTATGATGGTGACTTTAAGGTGCTTGCGTGCCTTCCATTTCCCTCAGATGTCCTTCCTGCACCGCTACTGAAGGCGTGGTGCGTAACGGCAAAAGCACTGCCGGACATCAGCGCTATCTCTGCTCTACTTGCCGTAAAACATGACAACTACAGTTCACTTACACCGCCTCTCAGCCCGGTACGCACCAGAAAATCATTGATATGGCCATgc                                                                                                                                                                                                                        >  2:244601/8‑249 (MQ=18)             gATTTCGGTAATGCTGCCAACTTACTGATTTAGTGTATGATGGTGATTTTAAGGTGCTTGCGTGGCTTCCATTTCCATCAGATGTCCTTCCGGCTCCGCTACTGAAGGCGTGGTGCGTAACGGCAAAAGCACTGCCGGACATCAGCGCTTTCTCGGCTCTCATTGCCGTAAAACATGGCAACTACAGTTCACTTACACCGCCTCTCAGCCCGGTACGCACCAGAAAATCATTGATATGGCCATGAATGGCg                                                                                                                                                                                                                  <  1:262374/251‑1 (MQ=255)                       aTGCGGCCAACTTACTGAGTTGGGTTATGATGGTGATTTTAAGGTGCTTGCGGGGCTTCCATTTCCATCAGATGTCCTTCCTGCTCCGCTACGGAAGGCGTGGTGCGTAACGGCAAAAGCACTGCCGGACATCAGCGCTATCTCTGCTCTCATTGCCGAAAAACATGGCAAGTACAGTTCATTTACACCGCCTCTCAGCCCGGTACGCACCAGAAAATCATTGATATGGCCATGAATGGCGTCGGATGTcg                                                                                                                                                                                                        <  2:102820/251‑1 (MQ=18)                            gcCAACTTACTGATTTAGTGTATGATGGTGATTTTAAGGTGCTTGCGTGGCTTCCATTTCCATCAGATGTCCTTCCTGCTCCGCTACTGAAGGCGTGGTGCGTAACGGCAAAAGCACTGCCGGACATCAGCGCTATCTCTGCTCTCATTGCCGTAAAACATGGCAACTACAGTTCACTTACACCGCCTCTCAGCCCGGTACGCACCAGAAAATCATTGATATGGCCATGAATGGCGTCGGATGTCGCGcc                                                                                                                                                                                                    >  1:174462/1‑250 (MQ=255)                                    aCTGATTTAGTGTATGATGGTGATTTTAAGGTGCTTGCGTGGCTTCCATTTCCATCAGATGTCCTTCCTGCTCCGCTACTGAAGGCGTGGTGCGTAACGGCAAAAGCACTGCCGGACATCAGCGCTATCTCTGCTCTCATTGCCGTAAAACATGGCAACTACAGTTCACTTACACCGCCTCTCAGCCCGGTACGCACCAGAAAATCATTGATATGGCCATGAATGGCGTCGGATGTCGCGCCAGTGCACGc                                                                                                                                                                                           >  2:83785/1‑251 (MQ=255)                                        aTTTAGGGTATGATGGTGATTTGAAGGTGCTGGCGTGGCTTCCATTTCCATCAGATGTCCTTCCGGCCCCGCTACTGAAGGCGTGGTGCGTAACGGCAAAAGCACTGCCGGACATCAGCGCTATCTCTGCTCTCATTGCCGTAAAACATGGCAACTACAGTTCACTTACACCGCCTCTCAGCCCGGTACGCACCAGAAAATCATTGATATGGCCATGAATGGCGTCGGATGTCGCGCCAGTGCACGCAtt                                                                                                                                                                                        <  2:174462/250‑1 (MQ=21)                                           tAGTGTATGATGGTGATTTTAAGGTGCTTGCGTGGCTTCCATTTCCATCAGATGTCCTTCCTGCTCCGCTACTGCAGGCGTGGTGCGTAACGGCAAAAGCACTGCCGGACATCAGCGCTATCTCTGCTCTCATTGCCGTAAAACATGGCAACTACAGTTCACTTACACCGCCTCTCAGCCCGGTACGCACCAGCAAATCATTGATATGGCCATGAATGGCGTCGGATGTCGTGCCAGTGCACGCATTATgg                                                                                                                                                                                    >  2:96725/1‑251 (MQ=255)                                                       gTGATTTTAAGGTGCTTGCGTGGCTTCAATTTCCATCAGACGTCCTTCCTGCTCCGCTACTGACGGCGTGGTGCGTAACGGCACAAGCACTGCCGGACATCAGCGCTATCTCTGCTCTCATTGCCGTAAAACATGGCAACTACAGTTCACTTACACCGCCTCTCAGCCCGGTACGCACCCGAAAATCATTGATATGGCCATGAATGGCGTCGGATGTCGCGCCAGTGCATGCATTATGGGCGTTGGCCTc                                                                                                                                                                         >  2:94292/1‑250 (MQ=21)                                                          aTTTTACGGTGCTTGCGTGGCTTCCATTTCAATCAGATGTCCTTCCTGCTCCGCTACTGAAGGCGTGGTGCGTAACGGCAAAAGCACTGCCGGACATCAGCGCTATCTCTGCTCTCATTGCCGTAAAACATGGCAACTACAGTTCACTTACACCGCCTCTCAGCCCGGTACGCACCAGAAAATCATTGATATGGCCATGAATGGCGTCGGATGTCGCGCCAGTGCACGCATTATGGGCGTTGGCCTCAac                                                                                                                                                                      >  1:75346/1‑250 (MQ=255)                                                                     cTTGCGTGGCTTCCATTTCCATCAGATGTCCTTCCTGCTCCGCTACTGAAGGCGTGGTGCGTAACGGCAAAAGCACTGCCGGACATCAGCGCTATCTCTGCTCTCATTGCCGTAAAACATGGCAACTACAGTTCACTTACACCGCCTCTCAGCCCGGTACGCACCAGAAAATCATTGATATGGCCATGAATGGCGTCGGATGTCGCGCCAGTGCACGCATTATGGGCGTTGGCCTCAACACGGTTTTACGt                                                                                                                                                          >  2:186220/1‑251 (MQ=255)                                                                               ttacatttccatCAGATGTCCTACCTGCTCCGCTACTGAAGGCGTGGTGCGTAACGGCAAAAGCACTGCCGGACATCAGGGCTATCTCTGCTCTCATTGCCGTAAAACATGGCAACTACAGTTCACTTACACCGCCTCTCAGACCGGTACGCACCAGAAAATCATTGATATGGCCATGAATGGCGTCGGCTGTCGCGCCAGTGCACGCATTATGGGCGTTGGCCTCAACATGGTTTAACGTAACTGaaaa                                                                                                                                                 >  1:151464/4‑250 (MQ=18)                                                                                              aTGTCTTTCCTGCCCCGCAACTGAAGGCGTGGTGCGTAACGGCAAAAGCACTGCCGGACATCAGCGCTATCTCTGCTCTCATTGCCGTAAAACATGGAAACAACAGTTCACTTACACCGCCTCTCAGCCCGGTACGCACCAGAAAATCATTGATATGGCCATGAATGTCGTCGGATGTCGCGCCAGTGCTCGCATTATGGGCGTTGGCTTCAACACGGTTGTACGTCACTTTAAAAACTCAGGCCGTAGTc                                                                                                                                 <  2:229472/251‑1 (MQ=17)                                                                                                                 acggAAGGCGTGGTGCGTAACGGCAAAAGCCCTGCCGGACATCAGCGCTACCTCTGCTCTAATTGCCGTAAAACATGACAACTACAGTTCACTTACACCGCCTCTCAGCCCGGTACGCACCAGAAAATCATTGATATGGCCATGAATGGCGTCGGATGTCGCGCCAGTGCACGCATTATGGGCGTTGGCCTCAACACGGTTTTACGTCACTTAAAAAACTCAGGCCGTAGTCGGTAACCTCGCGCATACaa                                                                                                              <  2:173355/248‑1 (MQ=17)                                                                                                                 aCTGAAGGCGTGGGGCGTAACGGCAAAACCACTGCCGGACATCAGCGCTATCTCTGCTCTCATTGCCGTAAAACATGGCAACTACAGTGCACTTACACCGCCTCTCAGCCCGGTACGCACCAGAAAATCATTGATATGGCCATGAATGGCGTCGGATGTCGCGCCAGTGCACGCATTATGGGCGTTGGCCTCAACACGGTTTTACGTCACTTAAAAAACTCAGGCCGTAGTCTGTAACCTCTCGCATACa                                                                                                               <  2:129003/250‑1 (MQ=17)                                                                                                                  cTGAAGGCGTGGTGCGTAACGGCAAAAGCACTGCCGGACATCAGCGCTATCTCTGCTCTCATTGCCGTAAAACATGGCAACTACAGTTCACTTACACCGCCTCTCAGCCCGGTACGCACCAGAAAATCATTGATATGGCCATGAATGGCGTCGGATGTCGCGCCAGTGCACGCATTATGGGCGTTGGCCTCAACACGGTTTTACGTCACTTAAAAAACTCAGGCCGTAGTCGGTAACCTCGCGCATACAAc                                                                                                             >  2:84395/1‑251 (MQ=255)                                                                                                                     aaGGCGTGGTGCGTAACGGCAAAAGCACTGCCGGACATCAGCGCTATCTCTGCTCTCATTGCCGTAAAACATGGCAACTACAGTTCACTTACACCGCCTCTCAGCCCGGTACGCACCAGAAAATCATTGATATGGCCATGAATGGCGTCGGATGTCGCGCCAGTGCACGCATTATGGGCGTTGGCCTCAACACGGTTTTACGTCACTTAAAAAACTCAGGCCGTAGTCGGTAACCTCGCGCATACAACCgg                                                                                                          >  1:128522/1‑251 (MQ=255)                                                                                                                              tgCGTAACGGCAAAAGCACTGCCGGACATCAGCGCTATCTCTGCTCTCATTGCCGTAAAACATGGCCACTACAGTTCACTTACACCGCCTCTCAGCCCGGTACGCCCCAGAAAATCATTGATATGGCCATGAATGGCGTCGGATGTCGCGCCAGTGCAAGCATTATGGGCGTTGGCCTCAACACGGTTTTACGTCACTTAAAAAACTCAGGCCGTAGTCGGTAACCTCGCGCATACAACCGGGCAgtgatg                                                                                                 >  1:257381/1‑251 (MQ=255)                                                                                                                                ggaaaCGGCAAAAGCACTGCCGGACATCAGCGCTATCCCTGCTCCAATGGCCGTAAAACATGGCAACTACAGTTAACTTACACCGCCTCTCAGCCCGGTACGCACCAGAAAATCATTGATATGGCCATGAATGGCGTCGGATGTCGCGCCAGTGCACGCATTATGGGCGTTGGCCTCAACACGGTTTTACGTCACTTAAAAAACTCAGGCCGTAGTCGGTAACCTCGCGCATACAACCGGGCAgtgatgtg                                                                                               <  2:78807/248‑1 (MQ=17)                                                                                                                                   aaCGGCAAAAGCACTGCCGGACATCAGCGCTATCTCTGCTCTCATTGCCGTAAAACATGGCAACTACAGTTCACTTACACCGCCTCTCAGCCCGGTACGCACCAGAAAATCATTGATATGGCCATGAATGGCGTCGGATGTCGCGCCAGTGCACGCATTATGGGCGTTGGCCTCAACACGGTTTTACGTCACTTAAAAAACTCAGGCCGTAGTCGGTAACCTCGCGCATACAACCGGGCAGTGATGTGAtt                                                                                            <  1:83785/251‑1 (MQ=255)                                                                                                                                               aCTGCCGGACATCAGCGCTATCTCTGCTCTCATTGCCGTAAAACATGGCAACTACAGTTCACTTACACCGCCTCTCAGCCCGGTACGCACCAGAAAATCATTGATATGGCCATGAATGGCGTCGGGTGTCGAGCCAGTGCACGCATTATGGGCGTGGGCCTCACCACGGTTTTACGTCACTTAAAAAACTCAGGCCGTAGTCGGGAACCTCGCGCATACAAcc                                                                                                            >  1:237195/1‑223 (MQ=17)                                                                                                                                                      gACATCAGCGCTATCTCTGCTCTCATTGCCGTAAAACATGGCAACTACAGTTCACTTACACCGCCTCTCAGCCCGGTACGCACCAGAAAATCATTGATATGGCCATGAATGGAGTCGGATGTCGCGCCAGTGCACGCATTATGGGCGTTGGCCTCAACACGGTTTTACGTCACTTAAAAAACTCAGGACGTAGTCGGTAACCTCGCGCATACAACCGGGAAGGGATGTGATTGTCTGCGCTGAAATGGACg                                                                         >  2:34299/1‑251 (MQ=18)                                                                                                                                                        cATCAGCGCTATCTCTGCTCTCATTGCCGTAAAACATGGCAACTACAGTTCACTTACACCGCCTCTCAGCCCGGTACGCACCAGAAAATCATTGATATGGCCATGAATGGCGTCGGATGTCGCGCCAGTGCACGCATTATGGGCGTTGGCCTCAACACGGTTTTACGTCACTTAAAAAACTCAGGCCGTAGTCGGTAACCTCGCGCATACAACCGGGCAGTGATGTGATTGTCTGCGCTGAAATGGACGa                                                                        >  1:97394/1‑250 (MQ=255)                                                                                                                                                                        tccctcattGCCGTAAAACAGGGCAACTCCAGTTCCCTAACACCGCCTCTCAGCCCGGTACGCACCAGAAAATCATTGATATGGCCATGAATGGCGTCGGATGTCGCGCCAGTGCACGCATTATGGGCGTTGGCCTCAACACGGTTTTACGTCACGTAAAAAACTCAGGCCGTAGTCGGTAACCTCGCGCATACAACCGGGCAGTGATGTGATTGTCTGCGCTGAAATGGACGAACAGTGGGGCTACGTc                                                        <  2:97394/243‑1 (MQ=18)                                                                                                                                                                                   cGTAAAACATGGCAACTACAGTTCACTTACAACGCCTCTCAGCCCGGTACGCACCAGAAAATCATTGATATGGCCATGAATGGCGTCGGATGTCGCGCCAGTGCACGCATTATGGGCGTTGGCCTCAACACGGTTTTACGTCACTTAAAAAACTCCGGCCGTAGTCGGTAACCTCGCGCATACAACCGGGCAGTGATGTGATTGTCTGCGCTGAAATGGACGAACAGTGGGGCTACGTCGGTGCTAAATcc                                            >  1:242142/1‑250 (MQ=255)                                                                                                                                                                                                    aCAGTTCACTTACACCGCCTCTCAGCCCGGTACGCACCAGAAAATCATTGATATGGCCATGAATGGCGTCGGATGTCGCGCCAGTGCACGCATTATGGGCGTTGGCCTCAACACGGTTTTACGTCACTTAAAACACTCAGGCCGTAGTCGGTAACCTCGCGCATACACCCGGGCAGTGATGTGATTGTCTGCGCTGAAATGGACGACCAGTGGGGCTACGTCGGTGCTAAATCACGTCAGCgctggctgct                           >  1:244934/1‑249 (MQ=255)                                                                                                                                                                                                            cTTACACCGCCTCTCAGCCCGGTACGCACCAGAAAATCATTGATATGGCCATGAATGGCGTCGGATGTCGCGCCAGTGCACGCATTATGGGCGTTGGCCTCAACACGGTTTTACGTCACTTAAAAAACTCAGGCCGTAGTCGGTAACCTCGCGCATACAACCGGGCAGTGATGTGATTGTCTGCGCTGAAATGGACGAACAGTGGGGCTACGTCGGTGCTAAATCACGTCAGCGCTGGCTGTTTTACGCGt                   >  1:244583/1‑251 (MQ=255)                                                                                                                                                                                                                    gCCTCTCAGCCCGGTACGCACCAGAAAATCATTGATATGGCCATGAATGGCGTCGGATGTCGCGCCAGTGCACGCATTATGGGCGTTGGCCTCAACACGGTTTTACGTCACTTAAAAAACTCAGGCCGTAGTCGGTAACCTCGCGCATACAACCGGGCAGTGATGTGATTGTCTGCGCTGAAATGGACGAACAGTGGGGCTACGTCGGTGCTAAATCACGTCAGCGCTGGCTGTTTTACGCGTATGACAgg           >  1:105694/1‑251 (MQ=255)                                                                                                                                                                                                                      ctctCAGCCCGGTACGCACCAGAAAATCATTGATATGGCCATGAATGGCGTCGGATGTCGCGCCAGTGCACGCATTATGGGCGTTGGCCTCAACACGGTTTTACGTCACTTAAAAAACTCAGGCCGTAGTCGGTAACCTCGCGCATACAACCGGGCAGAGATGTGATTGTCTGCGCTGAAATGGACGAACAGTGGGGCTACGTCGGTGCTAAATCACGTCAGCGCTGGCTGTTTTACGCGTCTGACAGGAt         >  1:187071/1‑251 (MQ=255)                                                                                                                                                                                                                              ccGGTACGCACCAGAAAATCATTGATATGGCCATGAATGGCGTCGGATGTCGCGCCAGTGCACGCATTATGGGCGTTGGCCTCAACACGGTTTTACGTCACTTAAAAAACTCAGGCCGTAGTCGGTAACCTCGCGCATACAACCGGGCAGTGATGTGATTGTCTGCGCTGAAATGGACGAACAGTGGGGCTACGTCGGTGCTAAATCACGTCAGCGCTGGCTGTTTTACGCGTATGACAGGATACggagg  >  2:81272/1‑250 (MQ=255)                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                                    CTAAAGGATGGGGATTTCGGTAATGCTGCCAACTTACTGATTTAGTGTATGATGGTGATTTTAAGGTGCTTGCGTGGCTTCCATTTCCATCAGATGTCCTTCCTGCTCCGCTACTGAAGGCGTGGTGCGTAACGGCAAAAGCACTGCCGGACATCAGCGCTATCTCTGCTCTCCTTGCCGTAAAACATGGCAACTACAGTTCACTTACACCGCCTCTCAGCCCGGTAAGCACCAGAAAATCATTGATATGGCCATGAATGGCGTCGGATGTCGCGCCAGTGCACGCATTATGGGCGTTGGCCTCAACACGGTTTTACGTCACTTAAAAAACTCAGGCCGCAGTCGGTAACCTCGCGCATACAACCGGGCAGTGATGTGATTGTCTGCGCTGAAATGGACGAACAGTGGGGCTACGTCGGTGCTAAATCACGTCAGCGCTGGCTGTTTTACGCGTATGACAGGATACGGAGG  >  NC_000913/4518454‑4518924

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑