Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,467,061	C→T	pseudogene (1670/2513 nt)	ydbA →	pseudogene, autotransporter homolog, interrupted by IS2 and IS30

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,467,061	0	C	T	100.0%	169.6 / NA	49	pseudogene (1670/2513 nt)	ydbA	pseudogene, autotransporter homolog, interrupted by IS2 and IS30
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (20/29);  total (20/29)

CAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAGGGGGCAACAGTATCCAATACGGGTG  >  NC_000913/1466925‑1467186                                                                                                                                         |                                                                                                                              cAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTgtgc                                                                                                                             <  2:774087/139‑1 (MQ=255)  aGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCa                                                                                                                            <  2:234827/139‑1 (MQ=255)         cGGTAACGACGCCACCGCGAATAACAATGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATg                                                                                                                          <  1:121417/134‑1 (MQ=255)         cGGTAACGACGCCACCGCGAATAACAATGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATg                                                                                                                          >  2:121417/1‑134 (MQ=255)            tAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTgag                                                                                                                  <  2:313228/139‑1 (MQ=255)             aaCGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGTACCAAAATCGCGTGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTgaga                                                                                                                 <  2:871684/139‑1 (MQ=255)              acgacgCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGaa                                                                                                                >  2:327782/1‑139 (MQ=255)                  cgCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACAtt                                                                                                            >  2:237872/1‑139 (MQ=255)                   gCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTg                                                                                                           >  2:186406/1‑139 (MQ=255)                   gCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGTACAAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTg                                                                                                           >  2:602087/1‑139 (MQ=255)                             aTAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACgg                                                                                                 <  1:162057/139‑1 (MQ=255)                               aaCAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCa                                                                                               <  2:363290/139‑1 (MQ=255)                                          aaCCACTGTTGATGGAAAAGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTaacaac                                                                                    <  1:359692/139‑1 (MQ=255)                                             cACTGTTGATGGAAAAGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACaaa                                                                                 <  2:961082/139‑1 (MQ=255)                                              aCTGTTGATGGAAAAGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCa                                                                                               <  1:633299/124‑1 (MQ=255)                                              aCTGTTGATGGAAAAGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCa                                                                                               >  2:633299/1‑124 (MQ=255)                                                    gATGGAAAAGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCa                                                                                               <  1:145519/118‑1 (MQ=255)                                                    gATGGAAAAGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCa                                                                                               >  2:145519/1‑118 (MQ=255)                                                     aTGGAAAAGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGatat                                                                         >  1:1036726/1‑139 (MQ=255)                                                          aaaGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATAttgttg                                                                    <  1:237872/139‑1 (MQ=255)                                                            aGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTgttgtt                                                                  >  2:328354/1‑139 (MQ=255)                                                              aTTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTc                                                                <  2:685425/139‑1 (MQ=255)                                                                                  gcgGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGa                                                                                                       >  1:575459/1‑80 (MQ=255)                                                                                  gcgGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGa                                                                                                       <  2:575459/80‑1 (MQ=255)                                                                                  gcgGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCg                                            <  1:572261/139‑1 (MQ=255)                                                                                  gcgGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCg                                            <  1:881515/139‑1 (MQ=255)                                                                                       cAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCtc                                       <  2:196149/139‑1 (MQ=255)                                                                                                     tAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAggg                         >  1:166342/1‑139 (MQ=255)                                                                                                      aaaTCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAgggg                        <  2:46201/139‑1 (MQ=255)                                                                                                          cTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAGGGGGCaa                    <  2:582750/139‑1 (MQ=255)                                                                                                          cTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAGGGGGCaa                    <  1:76446/139‑1 (MQ=255)                                                                                                             gATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCa                                                                                               >  2:288146/1‑61 (MQ=255)                                                                                                             gATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCa                                                                                               <  1:288146/61‑1 (MQ=255)                                                                                                               tGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAGGGGGCAACAGTa               >  1:1079610/1‑139 (MQ=255)                                                                                                                  tAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACa                                                                                                              >  2:74583/1‑41 (MQ=255)                                                                                                                  tAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACa                                                                                                              <  1:74583/41‑1 (MQ=255)                                                                                                                    gCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAGGGGGCAACAGTATCCaa          >  1:551021/1‑139 (MQ=255)                                                                                                                    gCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAGGGGGCAACAGTATCCaa          >  1:242495/1‑139 (MQ=255)                                                                                                                       tGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTc                                                                <  1:85553/82‑1 (MQ=255)                                                                                                                       tGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTc                                                                >  2:85553/1‑82 (MQ=255)                                                                                                                          cTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAGGGGGCAACAGTATCCAATACggg    <  1:328354/139‑1 (MQ=255)                                                                                                                          cTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAGGGGGCAACAGTATCCAATACggg    <  1:602087/139‑1 (MQ=255)                                                                                                                          cTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAGGGGGCAACAGTATCCAATACggg    <  2:1079610/139‑1 (MQ=255)                                                                                                                            gTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAGGGGGCAACAGTATc             <  2:290097/128‑1 (MQ=255)                                                                                                                            gTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAGGGGGCAACAGTATc             >  1:290097/1‑128 (MQ=255)                                                                                                                            gTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAGGGGGCAACAGTATCCAATACGGGTg  <  1:924166/139‑1 (MQ=255)                                                                                                                              tACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAGGGGGCAACAGTATCCAATACggg    <  2:372484/135‑1 (MQ=255)                                                                                                                              tACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAGGGGGCAACAGTATCCAATACggg    >  1:372484/1‑135 (MQ=255)                                                                                                                                   gCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTaacaa                                                                                     >  2:594140/1‑49 (MQ=255)                                                                                                                                   gCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTaacaa                                                                                     <  1:594140/49‑1 (MQ=255)                                                                                                                                         |                                                                                                                              CAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAGGGGGCAACAGTATCCAATACGGGTG  >  NC_000913/1466925‑1467186

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑