Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	393,298	T→C	pseudogene (329/1449 nt)	yaiT →	pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	393,298	0	T	C	100.0%	209.7 / NA	54	pseudogene (329/1449 nt)	yaiT	pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (21/33);  total (21/33)

GATCTGGTGAACGACCGTACCTGGGATACTTCCAAGTCTAACTACGGTTACGGTATTGTTGCTATGAACTCTGATGGTCACCTGACTATCAACGGTAACGGCGACGTAGACAACGGTACTGAACTGGATAACAGCTCTGTAGACAATGTTGTTGCTGCAACCGGTAACTACAAAGTTCGTATCGACAACGCAACTGGCGCTGGCGCTATCGCTGATTACAAAGATAAAGAAATTATCTACGTAAACGACGTCAACAGCAACGCGACCTTCTCTGCTGCTAACAA  >  NC_000913/393159‑393442                                                                                                                                            |                                                                                                                                                 gATCTGGTGAACGACCGTACCTGGGATACTTCCAAGTCTAACTACGGTTACGGTATTGTTGCTATGAACTCTGATGGTCACCTGACTATCAACGGTAACGGCGACGTAGACAACGGTACTGAACTGGATAACAGCTCTGCAGACAAtgtt                                                                                                                                        <  1:751128/150‑1 (MQ=255)      ggTGAACGACCGTACCTGGGATACTTCCAAGTCTAACTACGGTTACGGTATTGTTGCTATGAACTCTGATGGTCACCTGACTATCAACGGTAACGGCGACGTAGACAACGGTACTGAACTGGATAACAGCTCTGCAGACAATgttgtt                                                                                                                                     <  1:50748/148‑1 (MQ=255)      ggTGAACGACCGTACCTGGGATACTTCCAAGTCTAACTACGGTTACGGTATTGTTGCTATGAACTCTGATGGTCACCTGACTATCAACGGTAACGGCGACGTAGACAACGGTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTtgct                                                                                                                                  >  2:131552/1‑151 (MQ=255)          aaCGACCGTACCTGGGATACTTCCAAGTCTAACTACGGTTACGGTATTGTTGCTATGAACTCTGATGGTCACCTGACTATCAACGGTAACGGCGACGTAGACAACGGTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCaa                                                                                                                              <  2:94640/151‑1 (MQ=255)             gACCGTACCTGGGATACTTCCAAGTCTAACTACGGTTACGGTATTGTTGCTATGAACTCTGATGGTCACCTGACTATCAACGGTAACGGCGACGTAGACAACGGTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCg                                                                                                                           >  1:529351/1‑151 (MQ=255)              aCCGTACCTGGGATACTTCCAAGTCTAACTACGGTTACGGTATTGTTGCTATGAACTCTGATGGTCACCTGACTATCAACGGTAACGGCGACGTAGACAACGGTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCgg                                                                                                                          <  1:325723/151‑1 (MQ=255)              aCCGTACCTGGGATACTTCCAAGTCTAACTACGGTTACGGTATTGTTGCTATGAACTCTGATGGTCACCTGACTATCAACGGTAACGGCGACGTAGACAACGGTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCgg                                                                                                                          <  2:219080/151‑1 (MQ=255)               ccGTACCTGGGATACTTCCAAGTCTAACTACGGTTACGGTATTGTTGCTATGAACTCTGATGGTCACCTGACTATCAACGGTAACGGCGACGTAGACAACGGTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCGGt                                                                                                                         >  1:394318/1‑151 (MQ=255)                  tACCTGGGATACTTCCAAGTCTAACTACGGTTACGGTATTGTTGCTATGAACTCTGATGGTCACCTGACTATCAACGGTAACGGCGACGTAGACAACGGTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCGGTAAc                                                                                                                      >  1:434761/1‑151 (MQ=255)                    ccTGGGATACTTCCAAGTCTAACTACGGTTACGGTATTGTTGCTATGAACTCTGATGGTCACCTGACTATCAACGGTAACGGCGACGTAGACAACGGTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCGGTAACt                                                                                                                     <  1:496645/150‑1 (MQ=255)                       gggATACTTCCAAGTCTAACTACGGTTACGGTATTGTTGCTATGAACTCTGATGGTCACCTGACTATCAACGGTAACGGCGACGTAGACAACGGTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCGGTAACTACa                                                                                                                  >  2:747481/1‑150 (MQ=255)                             cTTCCAAGTCTAACTACGGTTACGGTATTGTTGCTATGAACTCTGATGGTCACCTGACTATCAACGGTAACGGCGACGTAGACAACGGTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCGGTAACTACAAAGTTCg                                                                                                           >  2:362236/1‑151 (MQ=255)                               tCCAAGTCTAACTACGGTTACGGTATTGTTGCTATGAACTCTGATGGTCACCTGACTATCAACGGTAACGGCGACGTAGACAACGGTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCGGTAACTACAAAGTTCGt                                                                                                          <  1:662561/150‑1 (MQ=255)                               tCCAAGTCTAACTACGGTTACGGTATTGTTGCTATGAACTCTGATGGTCACCTGACTATCAACGGTAACGGCGACGTAGACAACGGTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCGGTAACTACAAAGTTCGt                                                                                                          <  1:525009/150‑1 (MQ=255)                                ccAAGTCTAACTACGGTTACGGTATTGTTGCTATGAACTCTGATGGTCACCTGACTATCAACGGTAACGGCGACGTAGACAACGGTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCGGTAACTACAAAGTTCGTAt                                                                                                        >  1:517487/1‑151 (MQ=255)                                        aaCTACGGTTACGGTATTGTTGCTATGAACTCTGATGGTCACCTGACTATCAACGGTAACGGCGACGTAGACAACGGTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCGGTAACTACAAAGTTCGTATCGACaa                                                                                                  <  1:166520/149‑1 (MQ=255)                                        aaCTACGGTTACGGTATTGTTGCTATGAACTCTGATGGTCACCTGACTATCAACGGTAACGGCGACGTAGACAACGGTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCGGTAACTACAAAGTTCGTATCGACAAc                                                                                                 <  1:568001/150‑1 (MQ=255)                                           tacggttacggtATTGTTGCTATGAACTCTGATGGTCACCTGACTATCAACGGTAACGGCGACGTAGACAACGGTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCGGTAACTACAAAGTTCGTATCGACAACGCa                                                                                              >  1:56456/1‑150 (MQ=255)                                            acggttacggtATTGTTGCTATGAACTCTGATGGTCACCTGACTATCAACGGTAACGGCGACGTAGACAACGGTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCGGTAACTACAAAGTTCGTATCGACAACGCAAc                                                                                            >  2:185988/1‑151 (MQ=255)                                             cggttacggtATTGTTGCTATGAACTCTGATGGTCACCTGACTATCAACGGTAACGGCGACGTAGACAACGGTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCGGTAACTACAAAGTTCGTATCGACCACGCa                                                                                              <  2:648478/148‑1 (MQ=255)                                             cggttacggtATTGTTGCTATGAACTCTGATGGTCACCTGACTATCAACGGTAACGGCGACGTAGACAACGGTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCGGTAACTACAAAGTTCGTATCGACAACGCAAct                                                                                           >  1:28238/1‑151 (MQ=255)                                             cggttacggtATTGTTGCTATGAACTCTGATGGTCACCTGACTATCAACGGTAACGGCGACGTAGACAACGGTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCGGTAACTACAAAGTTCGTATCGACAACGCAAct                                                                                           <  1:11779/151‑1 (MQ=255)                                                 tacggtATTGTTGCTATGAACTCTGATGGTCACCTGACTATCAACGGTAACGGCGACGTAGACAACGGTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCGGTAACTACAAAGTTCGTATCGACAACGCAActggcg                                                                                       >  2:475566/1‑151 (MQ=255)                                                   cggtATTGTTGCTATGAACTCTGATGGTCACCTGACTATCAACGGTAACGGCGACGTAGACAACGGTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCGGTAACTACAAAGTTCGTATCGACAACGCAActggcgct                                                                                     <  2:502315/151‑1 (MQ=255)                                                     gtATTGTTGCTATGAACTCTGATGGTCACCTGACTATCAACGGTAACGGCGACGTAGACAACGGTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCGGTAACTACAAAGTTCGTATCGACAACGCAActggcgctgg                                                                                   <  1:758116/151‑1 (MQ=255)                                                             gCTATGAACTCTGATGGTCACCTGACTATCAACGGTAACGGCGACGTAGACAACGGTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCGGTAACTACAAAGTTCGTATCGACAACGCAACTGGCGCTGGCGCTATc                                                                            <  1:240021/150‑1 (MQ=255)                                                                aTGAACTCTGATGGTCACCTGACTATCAACGGTAACGGCGACGTAGACAACGGTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCGGTAACTACAAAGTTCGTATCGACAACGCAACTGGCGCTGGCGCTATCGCt                                                                         <  1:420796/150‑1 (MQ=255)                                                                aTGAACTCTGATGGTCACCTGACTATCAACGGTAACGGCGACGTAGACAACGGTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCGGTAACTACAAAGTTCGTATCGACAACGCAACTGGCGCTGGCGCTATCGCTg                                                                        <  2:759159/151‑1 (MQ=255)                                                                    aCTCTGATGGTCACCTGACTATCAACGGTAACGGCGACGTAGACAACGGTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCGGTAACTACAAAGTTCGTATCGACAACGCAACTGGCGCTGGCGCTATCGCTGATTa                                                                    <  2:422897/151‑1 (MQ=255)                                                                                aCCTGACTATCAACGGTAACGGCGACGTAGACAACGGTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCGGTAACTACAAAGTTCGTATCGACAACGCAACTGGCGCTGGCGCTATCGCTGATTACAAAGATAAAGa                                                        <  2:453415/151‑1 (MQ=255)                                                                                 ccTGACTATCAACGGTAACGGCGACGTAGACAACGGTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCGGTAACTACAAAGTTCGTATCGACATCGCAACTGGCGCTGGCGCTATCGCTGATGACAAAGAGaaa                                                          <  2:393481/148‑1 (MQ=255)                                                                                  cTGACTATCAACGGTAACGGCGACGTAGACAACGGTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCGGTAACTACAAAGTTCGTATCGACAACGCAACTGGCGCTGGCGCTATCGCTGATTACAAAGATAAAGaa                                                       >  2:446428/1‑150 (MQ=255)                                                                                    gACTATCAACGGTAACGGCGACGTAGACAACGGTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCGGTAACTACAAAGTTCGTATCGACAACGCAACTGGCGCTGGCGCTATCGCTGATTACAAAGATAAAGaaa                                                      <  1:30734/149‑1 (MQ=255)                                                                                    gACTATCAACGGTAACGGCGACGTAGACAACGGTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCGGTAACTACAAAGTTCGTATCGACAACGCAACTGGCGCTGGCGCTATCGCTGATTACAAAGATAAAGAAAtt                                                    >  1:760172/1‑151 (MQ=255)                                                                                        aTCAACGGTAACGGCGACGTAGACAACGGTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCGGTAACTACAAAGTTCGTATCGACAACGCAACTGGCGCTGGCGCTATCGCTGATTACAAAGATAAAGAAATTAt                                                  <  2:621844/149‑1 (MQ=255)                                                                                          cAACGGTAACGGCGACGTAGACAACGGTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCGGTAACTACAAAGTTCGTATCGACAACGCAACTGGCGCTGGCGCTATCGCTGATTACAAAGATAAAGAAATTATCTa                                               <  2:112401/150‑1 (MQ=255)                                                                                            aCGGTAACGGCGACGTAGACAACGGTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCGGTAACTACAAAGTTCGTATCGACAACGCAACTGGCGCTGGCGCTATCGCTGATTACAAAGATAAAGAAATTATCTACGt                                            <  2:754175/151‑1 (MQ=255)                                                                                               gTAACGGCGACGTAGACAACGGTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCGGTAACTACAAAGTTCGTATCGACAACGCAACTGGCGCTGGCGCTATCGCTGATTACAAAGATAAAGAAATTATCTACGTaaa                                         <  1:77677/151‑1 (MQ=255)                                                                                                  aCGGCGACGTAGACAACGGTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCGGTAACTACAAAGTTCGTATCGACAACGCAACTGGCGCTGGCGCTATCGCTGATTACAAAGATAAAGAAATTATCTACGTAAacga                                      <  1:401999/151‑1 (MQ=255)                                                                                                      cGACGTAGACAACGGTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCGGTAACTACAAAGTTCGTATCGACAACGCAACTGGCGCTGGCGCTATCGCTGATTACAAAGATAAAGAAATTATCTACGTAAACGACGTc                                  <  1:747526/151‑1 (MQ=255)                                                                                                       gACGTAGACAACGGTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCGGTAACTACAAAGTTCGTATCGACAACGCAACTGGCGCTGGCGCTATCGCTGATTACAAAGATAAAGAAATTATCTACGTAAACGACGTc                                  >  2:427806/1‑150 (MQ=255)                                                                                                         cGTAGACAACGGTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCGGTAACTACAAAGTTCGTATCGACAACGCAACTGGCGCTGGCGCTATCGCTGATTACAAAGATAAAGAAATTATCTACGTAAACGACGTCAAc                               <  1:135658/151‑1 (MQ=255)                                                                                                            aGACAACGGTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCGGTAACTACAAAGTTCGTATCGACAACGCAACTGGCGCTGGCGCTATCGCTGATTACAAAGATAAAGAAATTATCTACGTAAACGACGTCAACAg                             <  2:220213/150‑1 (MQ=255)                                                                                                            aGACAACGGTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCGGTAACTACAAAGTTCGTATCGACAACGCAACTGGCGCTGGCGCTATCGCTGATTACAAAGATAAAGAAATTATCTACGTAAACGACGTCAACAGc                            >  2:66143/1‑151 (MQ=255)                                                                                                             gACAACGGTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCGGTAACTACAAAGTTCGTATCGACAACGCAACTGGCGCTGGCGCTATCGCTGATTACAAAGATAAAGAAATTATCTACGTAAACGACGTCAACAGc                            >  2:546552/1‑150 (MQ=255)                                                                                                                 aCGGTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCGGTAACTACAAAGTTCGTATCGACAACGCAACTGGCGCTGGCGCTATCGCTGATTACAAAGATAAAGAAATTATCTACGTAAACGACGTCAACAGCAAcgc                       >  2:723278/1‑151 (MQ=255)                                                                                                                    gTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCGGTAACTACAAAGTTCGTATCGACAACGCAACTGGCGCTGGCGCTATCGCTGATTACAAAGATAAAGAAATTATCTACGTAAACGACGTCAACAGCAACGCGAc                    <  1:477143/151‑1 (MQ=255)                                                                                                                    gTACTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCGGTAACTACAAAGTTCGTATCGACAACGCAACTGGCGCTGGCGCTATCGCTGATTACAAAGATAAAGAAATTATCTACGTAAACGACGTCAACAGCAACGCGAc                    >  1:398702/1‑151 (MQ=255)                                                                                                                      aCTGAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCGGTAACTACAAAGTTCGTATCGACAACGCAACTGGCGCTGGCGCTATCGCTGATTACAAAGATAAAGAAATTATCTACGTAAACGACGTCAACAGCAACGCGACCt                  <  2:281233/151‑1 (MQ=255)                                                                                                                         gAACTGGATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCGGTAACTACAAAGTTCGTATCGACAACGCAACTGGCGCTGGCGCTATCGCTGATTACAAAGATAAAGAAATTATCTACGTAAACGACGTCAACAGCAACGCGACCTtc                <  2:563256/150‑1 (MQ=255)                                                                                                                              ggATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCGGTAACTACAAAGTTCGTATCGACAACGCAACTGGCGCTGGCGCTATCGCTGATTACAAAGATAAAGAAATTATCTACGTAAACGACGTCAACAGCAACGCGACCTTCTctg            <  1:323897/149‑1 (MQ=255)                                                                                                                               gATAACAGCTCTGCAGACAATGTTGTTGCTGCAACCGGTAACTACAAAGTTCGTATCGACAACGCAACTGGCGCTGGCGCTATCGCTGATTACAAAGATAAAGAAATTATCTACGTAAACGACGTCAACAGCAACGCGACCTTCTctgctg         >  1:526197/1‑151 (MQ=255)                                                                                                                                    cAGCTCTGCAGACAATGTTGTTGCTGCAACCGGTAACTACAAAGTTCGTATCGACAACGCAACTGGCGCTGGCGCTATCGCTGATTACAAAGATAAAGAAATTATCTACGTAAACGACGTCAACAGCAACGCGACCTTCTCTGCTGCTAAc    >  2:76524/1‑151 (MQ=255)                                                                                                                                        tctGCAGACAATGTTGTTGCTGCAACCGGTAACTACAAAGTTCGTATCGACAACGCAACTGGCGCTGGCGCTATCGCTGATTACAAAGATAAAGAAATTATCTACGTAAACGACGTCAACAGCAACGCGACCTTCTCTGCTGCTAACaa  >  2:321873/1‑149 (MQ=255)                                                                                                                                            |                                                                                                                                                 GATCTGGTGAACGACCGTACCTGGGATACTTCCAAGTCTAACTACGGTTACGGTATTGTTGCTATGAACTCTGATGGTCACCTGACTATCAACGGTAACGGCGACGTAGACAACGGTACTGAACTGGATAACAGCTCTGTAGACAATGTTGTTGCTGCAACCGGTAACTACAAAGTTCGTATCGACAACGCAACTGGCGCTGGCGCTATCGCTGATTACAAAGATAAAGAAATTATCTACGTAAACGACGTCAACAGCAACGCGACCTTCTCTGCTGCTAACAA  >  NC_000913/393159‑393442

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑