Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	2,984,282	(C)6→7	pseudogene (370/490 nt)	BW25113_RS14825 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	2,984,276	1	.	C	100.0%	131.0 / NA	36	pseudogene (364/490 nt)	BW25113_RS14825	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base C (21/15);  total (21/15)

TCTGCTATGAGCATATATAAATTTTCGATAACAGATGATTTAATGAGTATGGCTGTAAATGAACTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTAT‑CCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTATGAATCCAGGTCATACACATTAAGGCATT  >  NZ_CP009273/2984141‑2984408                                                                                                                                         |                                                                                                                                     tCTGCTATGAGCATATATAAATTTTCGATAACAGATGATTTAATGAGTATGGCTGTAAATGAACTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTAT‑ccc                                                                                                                                   >  2:189897/1‑139 (MQ=255)             atatatAAATTTTCGATAACAGATGATTTAAAGAGTATGGCTGTAAATGAACTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCAcc                                                                                                                        <  2:344704/139‑1 (MQ=255)               atataAATTTTCGATAACAGATGATTTAATGAGTATGGCTGTAAATGAACTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTAT‑cccccc                                                                                                                                >  2:548074/1‑128 (MQ=255)               atataAATTTTCGATAACAGATGATTTAATGAGTATGGCTGTAAATGAACTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTAT‑cccccc                                                                                                                                <  1:548074/128‑1 (MQ=255)                      ttttCGATAACAGATGATTTAATGAGTATGGCTGTAAATGAACTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACataa                                                                                                                >  1:393455/1‑138 (MQ=255)                          cGATAACAGATGATTTAATGAGTATGGCTGTAAATGAACTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACataata                                                                                                              >  2:48774/1‑136 (MQ=255)                                                tATGGCTGTAAATGAACTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTAc                                                                                     >  1:599494/1‑139 (MQ=255)                                                    gCTGTAAATGAACTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCt                                                                                  <  1:85594/138‑1 (MQ=255)                                                     cTGTAAATGAACTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTtc                                                                                >  2:288462/1‑139 (MQ=255)                                                        tAAATGAACTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTtctc                                                                              >  1:555683/1‑138 (MQ=255)                                                          aaTGAACTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCaa                                                                            >  2:109173/1‑138 (MQ=255)                                                                   aTAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACg                                                                                              >  2:481757/1‑111 (MQ=255)                                                                   aTAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACg                                                                                              <  1:481757/111‑1 (MQ=255)                                                                           gACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAAttt                                                          >  1:575766/1‑139 (MQ=255)                                                                                 aaTAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACa                                                                                                                   <  2:491647/76‑1 (MQ=255)                                                                                 aaTAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACa                                                                                                                   >  1:491647/1‑76 (MQ=255)                                                                                     gagaATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGaaaa                                                <  2:344487/139‑1 (MQ=255)                                                                                         ataatGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATg                                            <  2:575766/139‑1 (MQ=255)                                                                                           aatGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATc                                                                       <  1:494979/110‑1 (MQ=255)                                                                                           aatGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATc                                                                       >  2:494979/1‑110 (MQ=255)                                                                                             tGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCaa                                        >  2:537935/1‑139 (MQ=255)                                                                                                  aCCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGa                                    >  2:132998/1‑138 (MQ=255)                                                                                                  aCCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGAt                                   <  1:48774/139‑1 (MQ=255)                                                                                                       aaTAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTAt                              >  2:624644/1‑139 (MQ=255)                                                                                                              tCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGa                                    <  1:514608/126‑1 (MQ=255)                                                                                                              tCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGa                                    >  2:514608/1‑126 (MQ=255)                                                                                                                actactATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTATGAATCCAgg                     <  2:393455/139‑1 (MQ=255)                                                                                                                       tatGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTATGAATCCAGGTCATa                >  2:36111/1‑137 (MQ=255)                                                                                                                       tatGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTATGAATCCAGGTCATa                <  1:493696/137‑1 (MQ=255)                                                                                                                       tatGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTATGAATCCAGGTCATa                <  1:36111/137‑1 (MQ=255)                                                                                                                         tGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTATGAATCCAGGTCATa                >  2:483822/1‑135 (MQ=255)                                                                                                                         tGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTATGAATCCAGGTCATa                <  1:483822/135‑1 (MQ=255)                                                                                                                            acaGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTATGAATCCAGGTCATACACAtt          >  1:219004/1‑138 (MQ=255)                                                                                                                                aCGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTATGAATCCAGGTCATACACATTAAgg      >  1:506504/1‑138 (MQ=255)                                                                                                                                  gTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTATGAATCCAGGTCATACACATTAAGGCAt   <  2:127301/139‑1 (MQ=255)                                                                                                                                   ttCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTATGAATCCAGGTCATa                <  1:514161/125‑1 (MQ=255)                                                                                                                                   ttCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTATGAATCCAGGTCATa                >  2:514161/1‑125 (MQ=255)                                                                                                                                   ttCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTATGAATCCAGGTCATACACATTAAGGCAtt  >  1:605691/1‑139 (MQ=255)                                                                                                                                   ttCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTATGAATCCAGGTCATACACATTAAGGCAtt  >  1:210438/1‑139 (MQ=255)                                                                                                                                         |                                                                                                                                     TCTGCTATGAGCATATATAAATTTTCGATAACAGATGATTTAATGAGTATGGCTGTAAATGAACTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTAT‑CCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTATGAATCCAGGTCATACACATTAAGGCATT  >  NZ_CP009273/2984141‑2984408

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑