Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,940,160	Δ1 bp	coding (453/1428 nt)	hsrA ←	putative multidrug or homocysteine efflux system

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,940,157	0	G	.	100.0%	155.6 / NA	37	coding (456/1428 nt)	hsrA	putative multidrug or homocysteine efflux system
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base . (18/19);  total (18/19)

TGCGTCGTGCGGTGGTGAAATTGGGCATATGTTTGCGCGCGTAAAGAAGGCCCGCAATACCTATGGGGATATTGATTAAAAATATCCAGTGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAACGGGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGTTCATTACGAGGATAAGCGCGCAGTAAGGCCAGCCGAGCAACAGGCATCATCATTGCGCCGCCTATC  >  NC_000913/3940030‑3940283                                                                                                                                |                                                                                                                               tGCGTCGTGCGGTGGTGAAATTGGGCATATGTTTGCGCGCGTAAAGAAGGCCCGCAATACCTATGGGGATATTGATTAAAAATATCCAGTGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAAtt                                                                                                                    <  2:332614/139‑1 (MQ=255)          cGGTGGTGAAATTGGGCATATGTTTGCGCGCGTAAAGAAGGCCCGCAATACCTATGGGGATATTGATTAAAAATATCCAGTGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCccacc                                                                                                           <  1:1241/139‑1 (MQ=255)               gtgAAATTGGGCATATGTTTGCGCGCGTAAAGAAGGCCCGCAATACCTATGGGGATATTGATTAAAAATATCCAGTGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGAcc                                                                                                      >  2:298991/1‑139 (MQ=255)                          cATATGTTTGCGCGCGTAAAGAAGGCCCGCAATACCTATGGGGATATTGATTAAAAATATCCAGTGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGa                                                                                           <  1:317348/139‑1 (MQ=255)                          cATATGTTTGCGCGCGTAAAGAAGGCCCGCAATACCTATGGGGATATTGATTAAAAATATCCAGTGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGa                                                                                           >  2:540510/1‑139 (MQ=255)                                  tGCGCGCGTAAAGAAGGCCCGCAATACCTATGGGGATATTGATTAAAAATATCCAGTGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGc                                                                                                                 >  2:314477/1‑109 (MQ=255)                                  tGCGCGCGTAAAGAAGGCCCGCAATACCTATGGGGATATTGATTAAAAATATCCAGTGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGc                                                                                                                 <  1:314477/109‑1 (MQ=255)                                        cgTAAAGAAGGCCCGCAATACCTATGGGGATATTGATTAAAAATATCCAGTGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACt                                                                             >  1:375148/1‑139 (MQ=255)                                                  gCCCGCAATACCTATGGGGATATTGATTAAAAATATCCAGTGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGtt                                                                   <  2:133575/139‑1 (MQ=255)                                                  gCCCGCAATACCTATGGGGATATTGATTAAAAATATCCAGTGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGtt                                                                   <  2:354279/139‑1 (MQ=255)                                                     cGCAATACCTATGGGGATATTGATTAAAAATATCCAGTGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGTTCAt                                                                >  2:436294/1‑139 (MQ=255)                                                              tATGGGGATATTGATTAAAAATATCCAGTGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGTTCATTACGAGGAt                                                       <  1:540510/139‑1 (MQ=255)                                                                tGGGGATATTGATTAAAAATATCCAGTGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGTTCATTACGAGGATaa                                                     >  1:504252/1‑139 (MQ=255)                                                                  gggATATTGATTAAAAATATCCAGTGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGAC‑AAATTCAATACTGGAAGAAGTTCATTACGAGGATAAgcg                                                  >  2:496068/1‑139 (MQ=255)                                                                      tatTGATTAAAAATATCCAGTGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGTTCATTACGAGGATAAgcgcgc                                               >  2:569899/1‑139 (MQ=255)                                                                       atTGATTAAAAATATCCAGTGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCa                                                                                  >  2:245058/1‑103 (MQ=255)                                                                       atTGATTAAAAATATCCAGTGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCa                                                                                  <  1:245058/103‑1 (MQ=255)                                                                                     tCCAGTGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGTTCATTACGAGGATAAGCGCGCAGTAAGGCCAGCCGa                                >  2:275875/1‑139 (MQ=255)                                                                                         gTGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGTTCATTACGAGGATAAGCGCGCAGTAAGGCCAGCCGAGCaa                            <  2:375148/139‑1 (MQ=255)                                                                                          tGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGTTCATTACGAGGATAAGCGCGCAGTAAGGCCAGCCGAGCAAc                           >  1:258783/1‑139 (MQ=255)                                                                                          tGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGTTCATTACGAGGATAAGCGCGCAGTAAGGCCAGCCGAGCAAc                           >  2:262856/1‑139 (MQ=255)                                                                                           gCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGTTCATTACGAGGATAAGCGCGCAGTAAGGCCAGCCGAGCAACa                          <  1:275875/139‑1 (MQ=255)                                                                                           gCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGTTCATTACGAGGATAAGCGCGCAGTAAGGCCAGCCGAGCAACa                          <  1:23841/139‑1 (MQ=255)                                                                                           gCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGTTCATTACGAGGATAAGCGCGCAGTAAGGCCAGCCGAGCAACa                          <  2:710655/139‑1 (MQ=255)                                                                                                    cccAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGa                                                                                           >  2:190994/1‑65 (MQ=255)                                                                                                    cccAGGTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGa                                                                                           <  1:190994/65‑1 (MQ=255)                                                                                                         gTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGTTCATTACGAGGATAAGCGCGCAGTAAGGCCAGCCGAGCAACAGGTATCATCATTgc            >  2:520909/1‑139 (MQ=255)                                                                                                         gTGACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGTTCATTACGAGGATAAGCGCGCAGTAAGGCCAGCCGAGCAACAGGCATCATCATTgc            >  2:683108/1‑139 (MQ=255)                                                                                                           gACCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGTTCATTACGAGGATAAGCGCGCAGTAAGGCCAGCCGAGCAACAGGCATCATCATTgcgc          <  2:512179/139‑1 (MQ=255)                                                                                                            aCCAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGTTCATTACGAGGATAAGCGCGCAGTAAGGCCAGCCGAGCAACAGGCATCATCATTGcgcc         <  1:730458/139‑1 (MQ=255)                                                                                                              cAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACa                                                                                         <  1:582179/57‑1 (MQ=255)                                                                                                              cAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACa                                                                                         >  2:582179/1‑57 (MQ=255)                                                                                                              cAGCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGTTCATTACGAGGATAAGCGCGCAGTAAGGCCAGCCGAGCAACAGGCATCATCATTGcgccgc       >  2:288028/1‑139 (MQ=255)                                                                                                               aGCACGCCGCCAAAAAC‑GGGCCTAAAATTGGCCCCACCGACCCCGGCAGGGCGA‑AAAATTCAATACTGGAAGAAGTTCATTACGAGGATAAGCGCGCAGTAAGGCCAGCCGAGCAACAGGCATCATCATTGCGCCGCCt     <  1:496068/139‑1 (MQ=255)                                                                                                                gCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGTTCATTACGAGGATAAGCGCGCAGTAAGGCCAGCCGAGCAACAGGCATCATCATTGCGCCGCCt     <  1:32895/139‑1 (MQ=255)                                                                                                                gCACGCCGCCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGTTCATTACGAGGATAAGCGCGCAGTAAGGCCAGCCGAGCAACAGGCATCATCATTGCGCCGCCt     <  1:298991/139‑1 (MQ=255)                                                                                                                   cgccgcCAAGAAC‑GGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGTTCATTACGAGGATAAGCGCGCAGTAAGGCCAGCCGAGCAACAGGCATCATCATTGCGCCGCCTATc  >  1:413700/1‑139 (MQ=255)                                                                                                                                |                                                                                                                               TGCGTCGTGCGGTGGTGAAATTGGGCATATGTTTGCGCGCGTAAAGAAGGCCCGCAATACCTATGGGGATATTGATTAAAAATATCCAGTGCCAGGTTGCCCAGGTGACCAGCACGCCGCCAAGAACGGGGCCTAAAATTGGCCCCACCAGACCCGGCATGGCGACAAAATTCAATACTGGAAGAAGTTCATTACGAGGATAAGCGCGCAGTAAGGCCAGCCGAGCAACAGGCATCATCATTGCGCCGCCTATC  >  NC_000913/3940030‑3940283

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑