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%	95.9 / NA	27	pseudogene (364/490 nt)	BW25113_RS14825	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base C (14/13);  total (14/13)

TTTAATGAGTATGGCTGTAAATGAACTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTAT‑CCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTATGAATCCAGGTCATACACATTAAGGCATT  >  NZ_CP009273/2984179‑2984408                                                                                                   |                                                                                                                                     tttAATGAGTATGGCTGTAAATGAACTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACg                                                                                              <  1:422283/139‑1 (MQ=255) tttAATGAGTATGGCTGTAAATGAACTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACg                                                                                              <  2:425536/139‑1 (MQ=255)          tATGGCTGTAAATGAACTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAg                                                                                                                      >  2:322522/1‑106 (MQ=255)          tATGGCTGTAAATGAACTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAg                                                                                                                      <  1:322522/106‑1 (MQ=255)            tGGCTGTAAATGAACTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTAcc                                                                                    <  2:40941/138‑1 (MQ=255)                    aaTGAACTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACataata                                                                                                              <  1:128223/104‑1 (MQ=255)                    aaTGAACTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACataata                                                                                                              >  2:128223/1‑104 (MQ=255)                    aaTGAACTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGa                                                                                                          <  1:131363/108‑1 (MQ=255)                    aaTGAACTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGa                                                                                                          >  2:131363/1‑108 (MQ=255)                    aaTGAACTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTAT‑cccccccg                                                                                                                              >  1:15128/1‑85 (MQ=255)                    aaTGAACTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTAT‑cccccccg                                                                                                                              <  2:15128/87‑3 (MQ=255)                                     gACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAAttt                                                          >  2:328027/1‑139 (MQ=255)                                                  aataatGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAAt                                             >  1:33294/1‑139 (MQ=255)                                                     aatGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTAcc                                                                                    <  1:260432/97‑1 (MQ=255)                                                     aatGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTAcc                                                                                    >  2:260432/1‑97 (MQ=255)                                                              cTGAATAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATAc                                 >  1:455362/1‑139 (MQ=255)                                                                 aaTAAATTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAG‑AAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTAt                              >  2:375198/1‑138 (MQ=255)                                                                     aaTTCACTACTATATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTATGAAt                          <  1:328027/139‑1 (MQ=255)                                                                           ctactaTATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTATGAATCCAGGt                    >  1:146646/1‑139 (MQ=255)                                                                              ctaTATGCACAGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAG‑AAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTATGAATCCAGGTCATa                <  1:375198/139‑1 (MQ=255)                                                                                       caGACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTATGAATCCAGGTCATACACATTaa        <  2:455362/139‑1 (MQ=255)                                                                                         gACGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTATGAATCCAGGTCATACACATTAAgg      >  1:105205/1‑139 (MQ=255)                                                                                          aCGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTAt                              >  2:80673/1‑114 (MQ=255)                                                                                          aCGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTAt                              <  1:80673/114‑1 (MQ=255)                                                                                          aCGTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTATGAATCCAGGTCATACACATTAAgg      >  2:266135/1‑138 (MQ=255)                                                                                            gTTCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTATGAATCCAGGTCATACACATTAAGGCAt   <  2:444524/139‑1 (MQ=255)                                                                                             ttCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTATGAATCCAgg                     >  2:350862/1‑120 (MQ=255)                                                                                             ttCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTATGAATCCAgg                     <  1:350862/120‑1 (MQ=255)                                                                                             ttCTATCCCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTATGAATCCAGGTCATACACATTAAGGCAtt  >  1:125494/1‑139 (MQ=255)                                                                                                   |                                                                                                                                     TTTAATGAGTATGGCTGTAAATGAACTCATAAAACTGACCAAAATAGAGAATAATGTAGACCTGAATAAATTCACTACTATATGCACAGACGTTCTAT‑CCCCCCGCGTCACCAGACATAATAAAGAAAAAAACAAACGACATTCTACCCTTCTCAAAAATCCCCTTTTTAATTTTCATTGAAAAAATGGCAATTGATACTATGAATCCAGGTCATACACATTAAGGCATT  >  NZ_CP009273/2984179‑2984408

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑