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%	156.9 / NA	42	pseudogene (364/490 nt)	BW25113_RS14825	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base C (22/20);  total (22/20)

TGCTATGAGCATATATAAATTTTCGATAACAGATGATTTAATGAGTATGGCTGTAAATGAACTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTAT‑CCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTATGAATCCAGGTCATACACATTAAGGCATT  >  NZ_CP009273/2984143‑2984408                                                                                                                                       |                                                                                                                                     tGCTATGAGCATATATAAATTTTCGATAACAGATGATTTAATGAGTATGGCTGTAAATGAACTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTAT‑ccccc                                                                                                                                 >  2:526884/1‑139 (MQ=255)      tGAGCATATATAAATTTTCGATAACAGATGATTTAATGAGTATGGCTGTAAATGAACTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTAT‑cccccccgcg                                                                                                                            >  2:552094/1‑135 (MQ=255)             atataAATTTTCGATAACAGATGATTTAATGAGTATGGCTGTAAATGAACTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCAc                                                                                                                         >  1:477885/1‑136 (MQ=255)             atataAATTTTCGATAACAGATGATTTAATGAGTATGGCTGTAAATGAACTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCAc                                                                                                                         >  2:475010/1‑136 (MQ=255)             atataAATTTTCGATAACAGATGATTTAATGAGTATGGCTGTAAATGAACTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCAc                                                                                                                         >  2:327827/1‑136 (MQ=255)                                    atTTAATGAGTATGGCTGTAAATGAACTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAaaacaaac                                                                                               <  1:327827/139‑1 (MQ=255)                                     tttAATGAGTATGGCTGTAAATGAACTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACg                                                                                              <  1:475010/139‑1 (MQ=255)                                              tATGGCTGTAAATGAACTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTAc                                                                                     >  2:201146/1‑139 (MQ=255)                                                      tAAATGAACTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTtctc                                                                              >  1:95172/1‑138 (MQ=255)                                                      tAAATGAACTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTtctc                                                                              >  1:460989/1‑138 (MQ=255)                                                      tAAATGAACTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTtctc                                                                              >  1:339751/1‑138 (MQ=255)                                                              cTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATccc                                                                     >  1:187247/1‑139 (MQ=255)                                                                         gACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAAttt                                                          >  2:72364/1‑139 (MQ=255)                                                                           ccAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAAtttt                                                         >  1:298365/1‑138 (MQ=255)                                                                                      aataatGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAAt                                             >  1:405719/1‑139 (MQ=255)                                                                                           tGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAaaacaaa                                                                                                >  2:481429/1‑83 (MQ=255)                                                                                           tGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAaaacaaa                                                                                                <  1:481429/83‑1 (MQ=255)                                                                                           tGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCaa                                        >  2:464186/1‑139 (MQ=255)                                                                                           tGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCaa                                        >  2:322531/1‑139 (MQ=255)                                                                                             tAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATc                                                                       <  1:191257/106‑1 (MQ=255)                                                                                             tAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATc                                                                       >  2:191257/1‑106 (MQ=255)                                                                                             tAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAAtt                                      <  2:298365/139‑1 (MQ=255)                                                                                                aCCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGAt                                   <  2:339751/139‑1 (MQ=255)                                                                                                     aaTAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCaaaaa                                                                         >  1:295518/1‑96 (MQ=255)                                                                                                     aaTAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCaaaaa                                                                         <  2:295518/96‑1 (MQ=255)                                                                                                     aaTAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTAt                              >  1:55261/1‑139 (MQ=255)                                                                                                              actactATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTATGAATCCAgg                     <  1:552094/139‑1 (MQ=255)                                                                                                                     tatGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTATGAATCCAGGTCATa                <  1:72364/137‑1 (MQ=255)                                                                                                                     tatGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTATGAATCCAGGTCATa                <  1:244366/137‑1 (MQ=255)                                                                                                                     tatGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTATGAATCCAGGTCATa                <  1:111041/137‑1 (MQ=255)                                                                                                                     tatGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTATGAATCCAGGTCATa                <  1:247429/137‑1 (MQ=255)                                                                                                                     tatGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTATGAATCCAGGTCATa                <  2:405719/137‑1 (MQ=255)                                                                                                                           caGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTATGAATCCAGGTCATACACATTaa        <  1:464186/139‑1 (MQ=255)                                                                                                                           caGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTATGAATCCAGGTCATACACATTaa        <  1:322531/139‑1 (MQ=255)                                                                                                                            aGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAaaacaaa                                                                                                <  2:29358/50‑1 (MQ=255)                                                                                                                            aGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAaaacaaa                                                                                                >  1:29358/1‑50 (MQ=255)                                                                                                                            aGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGc                                          >  1:328280/1‑104 (MQ=255)                                                                                                                            aGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGc                                          <  2:328280/104‑1 (MQ=255)                                                                                                                             gACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTATGAATCCa                       <  2:343211/122‑1 (MQ=255)                                                                                                                             gACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTATGAATCCa                       >  1:343211/1‑122 (MQ=255)                                                                                                                             gACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTATGAATCCAGGTCATACACATTAAgg      <  1:201146/139‑1 (MQ=255)                                                                                                                              aCGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTATGAATcc                        >  2:114113/1‑120 (MQ=255)                                                                                                                              aCGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTATGAATcc                        <  1:114113/120‑1 (MQ=255)                                                                                                                                 ttCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTATGAATCCAGGTCATACACATTAAGGCAtt  >  2:236820/1‑139 (MQ=255)                                                                                                                                       |                                                                                                                                     TGCTATGAGCATATATAAATTTTCGATAACAGATGATTTAATGAGTATGGCTGTAAATGAACTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTAT‑CCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTATGAATCCAGGTCATACACATTAAGGCATT  >  NZ_CP009273/2984143‑2984408

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑