Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	734,002	T→C	pseudogene (455/759 nt)	ybfD →	ISAs1 family transposase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	734,002	0	T	C	93.2%	174.5 / 3.7	59	pseudogene (455/759 nt)	ybfD	ISAs1 family transposase
Reads supporting (aligned to +/- strand):  ref base T (2/2);  new base C (29/26);  total (31/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

TTGATGGAAAAATACACCGGCATTCTTATGACAAGAGTCGCCGTAAGGGAGCGATTCATGTCATTAGTGCGTTCTCAACAATGCACAGTCTGGTCATCGGACAGATCAAGACGGATAAGAAATCCAATGAGATCACAGCTATCCCTGAACTTCTTAACATGCTGGATATTAAAGGAAAAATCATCAAAACCGATGCGATGGGTTGCCAGAAAGATATTGCAGAGAAGATACAAAAACAGGGAGGTGATTATTTATTCGCTGTAAAAG  >  NZ_CP009273/733870‑734136                                                                                                                                     |                                                                                                                                       ttGATGGAAAAATACACCGGCATTCTTATGACAAGAGTCGCCGTAAGGGAGCGATTCATGTCATTAGTGCGTTCTCAACAATGCACAGTCTGGTCATCGGACAGATCAAGACGGATAAGAAATCCAATGAGACCACAGc                                                                                                                                  <  1:248393/139‑1 (MQ=255)         aaaaTACACCGGCATTCTTATGACAAGAGTCGCCGTAAGGGAGCGATTCATGTCATTAGTGCGTTCTCAACAATGCACAGTCTGGTCATCGGACAGATCAAGACGGATAAGAAATCCAATGAGACCACAGCTATCCCt                                                                                                                           >  1:1136116/1‑138 (MQ=255)         aaaaTACACCGGCATTCTTATGACAAGAGTCGCCGTAAGGGAGCGATTCATGTCATTAGTGCGTTCTCAACAATGCACAGTCTGGTCATCGGACAGATCAAGACGGATAAGAAATCCAATGAGACCACAGCTATCCCt                                                                                                                           >  2:277742/1‑138 (MQ=255)         aaaaTACACCGGCATTCTTATGACAAGAGTCGCCGTAAGGGAGCGATTCATGTCATTAGTGCGTTCTCAACAATGCACAGTCTGGTCATCGGACAGATCAAGACGGATAAGAAATCCAATGAGACCACAGCTATCCCTg                                                                                                                          <  1:296178/139‑1 (MQ=255)           aaTACACCGGCATTCTTATGACAAGAGTCGCCGTAAGGGAGCGATTCATGTCATTAGTGCGTTCTCAACAATGCACAGTCTGGTCATCGGACAGATCAAGACGGATAAGAAATCCAATGAGACCACAGCTATCCCTGaa                                                                                                                        <  1:205251/139‑1 (MQ=255)                  cGGCATTCTTATGACAAGAGTCGCCGTAAGGGAGCGATTCATGTCATTAGTGCGTTCTCAACAATGCACAGTCTGGTCATCGGACAGATCAAGACGGATAAGAAATCCAATGAGACCACAGCTATCCCTGAActtctt                                                                                                                  >  1:1285327/1‑138 (MQ=255)                    gCATTCTTATGACAAGAGTCGCCGTAAGGGAGCGATTCATGTCATTAGTGCGTTCTCAACAATGCACAGTCTGGTCATCGGACAGATCAAGACGGATAAGAAATCCAATGAGACCACAGCTATCCCTGAACTTCTTAAc                                                                                                               <  1:724020/139‑1 (MQ=255)                     cATTCTTATGACAAGAGTCGCCGTAAGGGAGCGATTCATGTCATTAGTGCGTTCTCAACAATGCACAGTCTGGTCATCGGACAGATCAAGACGGATAAGAAATCCAATGAGACCACAGCTATCCCTGAACTTCTTAACa                                                                                                              <  1:870180/139‑1 (MQ=255)                     cATTCTTATGACAAGAGTCGCCGTAAGGGAGCGATTCATGTCATTAGTGCGTTCTCAACAATGCACAGTCTGGTCATCGGACAGATCAAGACGGATAAGAAATCCAATGAGACCACAGCTATCCCTGAACTTCTTAACa                                                                                                              >  2:757671/1‑139 (MQ=255)                       ttCTTATGACAAGAGTCGCCGTAAGGGAGCGATTCATGTCATTAGTGCGTTCTCAACAATGCACAGTCTGGTCATCGGACAGATCAAGACGGATAAGAAATCCAATGAGACCACAGCTATCCCTGAACTTCTTAACATg                                                                                                            <  2:1077972/139‑1 (MQ=38)                       ttCTTATGACAAGAGTCGCCGTAAGGGAGCGATTCATGTCATTAGTGCGTTCTCAACAATGCACAGTCTGGTCATCGGACAGATCAAGACGGATAAGAAATCCAATGAGACCACAGCTATCCCTGAACTTCTTAACATg                                                                                                            >  1:682941/1‑139 (MQ=38)                       ttCTTATGACAAGAGTCGCCGTAAGGGAGCGATTCATGTCATTAGTGCGTTCTCAACAATGCACAGTCTGGTCATCGGACAGATCAAGACGGATAAGAAATCCAATGAGACCACAGCTATCCCTGAACTTCTTAACATg                                                                                                            <  2:921606/139‑1 (MQ=38)                            aTGACAAGAGTCGCCGTAAGGGAGCGATTCATGTCATTAGTGCGTTCTCAACAATGCACAGTCTGGTCATCGGACAGATCAAGACGGATAAGAAATCCAATGAGACCACAGCTATCCCTGAACTTCTTAACATGCt                                                                                                          <  1:277742/136‑1 (MQ=37)                            aTGACAAGAGTCGCCGTAAGGGAGCGATTCATGTCATTAGTGCGTTCTCAACAATGCACAGTCTGGTCATCGGACAGATCAAGACGGATAAGAAATCCAATGAGACCACAGCTATCCCTGAACTTCTTAACATGCt                                                                                                          <  2:682941/136‑1 (MQ=37)                               aCAAGAGTCGCCGTAAGGGAGCGATTCATGTCATTAGTGCGTTCTCAACAATGCACAGTCTGGTCATCGGACAGATCAAGACGGATAAGAAATCCAATGAGACCACAGCTATCCCTGAACTTCTTAACATGCTGGatat                                                                                                    >  2:828107/1‑139 (MQ=37)                                        gCCGTAAGGGAGCGATTCATGTCATTAGTGCGTTCTCAACAATGCACAGTCTGGTCATCGGACAGATCAAGACGGATAAGAAATCCAATGAGACCACAGCTATCCCTGAACTTCTTAACATGCTGGATATTAAAGGaa                                                                                            >  2:182025/1‑138 (MQ=37)                                          cGTAAGGGAGCGATTCATGTCATTAGTGCGTTCTCAACAATGCACAGTCTGGTCATCGGACAGATCAAGACGGATAAGAAATCCAATGAGACCACAGCTATCCCTGAACTTCTTAACATGCTGGATATTAAAGGaaaaa                                                                                         >  1:600247/1‑139 (MQ=37)                                                    cGATTCATGTCATTAGTGCGTTCTCAACAATGCACAGTCTGGTCATCGGACAGATCAAGACGGATAAGAAATCCAATGAGATCACAGCTATCCCTGAACTTCTTAACATg                                                                                                            <  2:89388/110‑1 (MQ=32)                                                    cGATTCATGTCATTAGTGCGTTCTCAACAATGCACAGTCTGGTCATCGGACAGATCAAGACGGATAAGAAATCCAATGAGATCACAGCTATCCCTGAACTTCTTAACATg                                                                                                            >  1:89388/1‑110 (MQ=32)                                                     gATTCATGTCATTAGTGCGTTCTCAACAATGCACAGTCTGGTCATCGGACAGATCAAGACGGATAAGAAATCCAATGAGACCACAGCTATCCCTGAACTTCTTAACATGCTGGATATTAAAGGAAAAATCATCAAAAcc                                                                              <  2:568866/139‑1 (MQ=25)                                                      aTTCATGTCATTAGTGCGTTCTCAACAATGCACAGTCTGGTCATCGGACAGATCAAGACGGATAAGAAATCCAATGAGACCACAGCTATCCCTGAACTTCTTAACATGCTGGATATTAAAGGAAAAATCATCAAAACcg                                                                             <  1:744218/139‑1 (MQ=37)                                                          aTGTCATTAGTGCGTTCTCAACAATGCACAGTCTGGTCATCGGACAGATCAAGACGGATAAGAAATCCAATGAGACCACAGCTATCCCTGAACTTCTTAACATGCTGGATATTAAAGGAAAAATCATCAAAACcgatgc                                                                         <  2:393604/139‑1 (MQ=37)                                                             tCATTAGTGCGTTCTCAACAATGCACAGTCTGGTCATCGGACAGATCAAGACGGATAAGAAATCCAATGAGACCACAGCTATCCCTGAACTTCTTAACATGCTGGATATTAAAGGAAAAATCATCAAAACcgatgcga                                                                       <  2:1136116/138‑1 (MQ=37)                                                                      cGTTCTCAACAATGCACAGTCTGGTCATCGGACAGATCAAGACGGATAAGAAATCCAATGAGACCACAGCTATCCCTGAACTTCTTAACATGCTGGATATTAAAGGAAAAATCATCAAAACCGATGCGATGGGTTGc                                                               >  2:1072717/1‑137 (MQ=37)                                                                        ttCTCAACAATGCACAGTCTGGTCATCGGACAGATCAAGACGGATAAGAAATCCAATGAGACCACAGCTATCCCTGAACTTCTTAACATGCTGGATATTAAAGGAAAAATCATCAAAACCGATGCGATGGGTTGCCAg                                                            >  1:176128/1‑138 (MQ=37)                                                                         tctcAACAATGCACAGTCTGGTCATCGGACAGATCAAGACGGATAAGAAATCCAATGAGACCACAGCTATCCCTGAACTTCTTAACATGCTGGATATTAAAGGAAAAATCATCAAAACCGATGCGATGGGTTGCCAGa                                                           >  1:356108/1‑138 (MQ=37)                                                                          ctcAACAATGCACAGTCTGGTCATCGGACAGATCAAGACGGATAAGAAATCCAATGAGACCACAGCTATCCCTGAACTTCTTAACATGCTGGATATTAAAGGAAAAATCATCAAAACCGATGCGATGGGTTGCCAGaa                                                          <  2:718255/138‑1 (MQ=37)                                                                                  tGCACAGTCTGGTCATCGGACAGATCAAGACGGATAAGAAATCCAATGAGACCACAGCTATCCCTGAACTTCTTAACATGCTGGATATTAAAGGAAAAATCATCAAAACCGATGCGATggg                                                                   <  1:1129925/121‑1 (MQ=38)                                                                                  tGCACAGTCTGGTCATCGGACAGATCAAGACGGATAAGAAATCCAATGAGACCACAGCTATCCCTGAACTTCTTAACATGCTGGATATTAAAGGAAAAATCATCAAAACCGATGCGATggg                                                                   >  2:1129925/1‑121 (MQ=38)                                                                                  tGCACAGTCTGGTCATCGGACAGATCAAGACGGATAAGAAATCCAATGAGACCACAGCTATCCCTGAACTTCTTAACATGCTGGATATTAAAGGAAAAATCATCAAAACCGATGCGATGGGTTGCCAGAAAGATATTg                                                  >  1:1166109/1‑138 (MQ=37)                                                                                      caGTCTGGTCATCGGACAGATCAAGACGGATAAGAAATCCAATGAGACCACAGCTATCCCTGAACTTCTTAACATGCTGGATATTAAAGGAAAAATCATCAAAACCGATGCGATGGGTTGCCAGAAAGATATTGCagag                                             <  1:1264322/139‑1 (MQ=37)                                                                                       aGTCTGGTCATCGGACAGATCAAGACGGATAAGAAATCCAATGAGACCACAGCTATCCCTGAACTTCTTAACATGCTGGATATTAAAGGAAAAATCATCAAAACCGATGCGATGGGTTGCCAGAAAGATATTGCagag                                             >  1:1139788/1‑138 (MQ=37)                                                                                         tCTGGTCATCGGACAGATCAAGACGGATAAGAAATCCAATGAGACCACAGCTATCCCTGAACTTCTTAACATGCTGGATATTAAAGGAAAAATCATCAAAACCGATGCGATGGGTTGCCAGAAAGATATTGCagag                                             >  1:53155/1‑136 (MQ=37)                                                                                              tCATCGGACAGATCAAGACGGATAAGAAATCCAATGAGACCACAGCTATCCCTGAACTTCTTAACATGCTGGATATTAAAGGAAAAATCATCAAAACcg                                                                             <  2:995341/99‑1 (MQ=255)                                                                                              tCATCGGACAGATCAAGACGGATAAGAAATCCAATGAGACCACAGCTATCCCTGAACTTCTTAACATGCTGGATATTAAAGGAAAAATCATCAAAACcg                                                                             >  1:995341/1‑99 (MQ=255)                                                                                                  cGGACAGATCAAGACGGATAAGAAATCCAATGAGACCACAGCTATCCCTGAACTTCTTAACATGCTGGATATTAAAGGAAAAATCATCAAAACCGATGCGATGGGTTGCCAGAAAGATATTGCAGAGAAGATACaaaaa                                 >  1:741400/1‑139 (MQ=37)                                                                                                   ggACAGATCAAGCCGGATAAGAAATCCAATGAGACCACAGCTATCCCTGAACTTCTTAACATGCTGGATATTAAAGGAAAAATCATCAAAACCGATGCGATGGGTTGCCAGAAAGATATTGCAGAGAAGATACaaaaa                                 >  1:450917/1‑138 (MQ=255)                                                                                                   ggACAGATCAAGACGGATAAGAAATCCAATGAGACCACAGCTATCCCt                                                                                                                           <  2:974594/48‑1 (MQ=255)                                                                                                   ggACAGATCAAGACGGATAAGAAATCCAATGAGACCACAGCTATCCCt                                                                                                                           >  1:974594/1‑48 (MQ=255)                                                                                                   ggACAGATCAAGACGGATAAGAAATCCAATGAGACCACAGCTATCCCTGAACTTCTTAACATGCTGGATATTAAAGGAAAAATCATCAAAACCGATGCGATGGGTTGCCAGAAAGATATTGCAGAGAAGATACaaaaa                                 >  2:715682/1‑138 (MQ=37)                                                                                                   ggACAGATCAAGACGGATAAGAAATCCAATGAGACCACAGCTATCCCTGAACTTCTTAACATGCTGGATATTAAAGGAAAAATCATCAAAACCGATGCGATGGGTTGCCAGAAAGATATTGCAGAGAAGATACaaaaa                                 <  2:1067548/138‑1 (MQ=37)                                                                                                      cAGATCAAGACGGATAAGAAATCCAATGAGACCACAGCTATCCCTGAACTTCTTAACATGCTGGATATTAAAGGAAAAATCATCAAAACCGATGCGATGGGTTGCCAGAAAGATATTGCAGAGAAGATACAAAAACAgg                             <  2:1285327/139‑1 (MQ=21)                                                                                                       aGATCAAGACGGATAAGAAATCCAATGAGACCACAGCTATCCCTGAACTTCTTAACATGCTGGATATTAAAGGAAAAATCATCAAAACCGATGCGATGGGTTGCCAGAAAGATATTGCAGAGAAGATACAAAAACAgg                             >  2:566287/1‑138 (MQ=21)                                                                                                        gATCAAGACGGATAAGAAATCCAATGAGATCACAGCTATCCCTGAACTTCTTAACATGCTGGATATTAAAGGAAAAATCATCAAAACCGATGCGATGGGTTGCCAGAAAGATATTGCAGAGAAGATACAAAAACAGGGa                           <  1:865668/139‑1 (MQ=34)                                                                                                        gATCAAGACGGATAAGAAATCCAATGAGACCACAGCTATCCCTGAACTTCTTAACATGCTGGATATTAAAGGAAAAATCATCAAAACCGATGCGATGGGTTGCCAGAAAGATATTGCAGAGAAGATACAAAAACAgg                             >  1:931961/1‑137 (MQ=21)                                                                                                                   aTAAGAAATCCAATGAGACCACAGCTATCCCTGAACTTCTTAACATGCTGGATATTAAAGGAAAAATCATCAAAACCGATGCGATGGGTTGCCAGAAAGATATTGCAGAGAAGATACaaaaa                                 <  1:636647/122‑1 (MQ=25)                                                                                                                   aTAAGAAATCCAATGAGACCACAGCTATCCCTGAACTTCTTAACATGCTGGATATTAAAGGAAAAATCATCAAAACCGATGCGATGGGTTGCCAGAAAGATATTGCAGAGAAGATACaaaaa                                 >  2:636647/1‑122 (MQ=25)                                                                                                                   aTAAGAAATCCAATGAGACCACAGCTATCCCTGAACTTCTTAACATGCTGGATATTAAAGGAAAAATCATCAAAACCGATGCGATGGGTTGCCAGAAAGATATTGCAGAGAAGATACAAAAACAGGGAGGTGattatt                 >  2:362729/1‑138 (MQ=21)                                                                                                                   aTAAGAAATCCAATGAGACCACAGCTATCCCTGAACTTCTTAACATGCTGGATATTAAAGGAAAAATCATCAAAACCGATGCGATGGGTTGCCAGAAAGATATTGCAGAGAAGATACAAAAACAGGGAGGTGattatt                 >  2:213352/1‑138 (MQ=21)                                                                                                                   aTAAGAAATCCAATGAGACCACAGCTATCCCTGAACTTCTTAACATGCTGGATATTAAAGGAAAAATCATCAAAACCGATGCGATGGGTTGCCAGAAAGATATTGCAGAGAAGATACAAAAACAGGGAGGTGattatt                 >  2:1003222/1‑138 (MQ=21)                                                                                                                   aTAAGAAATCCAATGAGACCACAGCTATCCCTGAACTTCTTAACATGCTGGATATTAAAGGAAAAATCATCAAAACCGATGCGATGGGTTGCCAGAAAGATATTGCAGAGAAGATACAAAAACAGGGAGGTGattatt                 >  1:521354/1‑138 (MQ=21)                                                                                                                   aTAAGAAATCCAATGAGACCACAGCTATCCCTGAACTTCTTAACATGCTGGATATTAAAGGAAAAATCATCAAAACCGATGCGATGGGTTGCCAGAAAGATATTGCAGAGAAGATACAAAAACAGGGAGGTGattatt                 >  2:722660/1‑138 (MQ=21)                                                                                                                      aGAAATCCAATGAGACCACAGCTATCCCTGAACTTCTTAACATGCTGGATATTAAAGGAAAAATCATCAAAACCGATGCGATGGGTTGCCAGAAAGATATTGCAGAGAAGATACAAAAACAGGGAGGTGATtatttatt             <  2:600247/139‑1 (MQ=21)                                                                                                                      aGAAATCCAATGAGACCACAGCTATCCCTGAACTTCTTAACATGCTGGATATTAAAGGAAAAATCATCAAAACCGATGCGATGGGTTGCCAGAAAGATATTGCAGAGAAGATACAAAAACAGGGAGGTGATtatttatt             <  2:741400/139‑1 (MQ=21)                                                                                                                      aGAAATCCAATGAGACCACAGCTATCCCTGAACTTCTTAACATGCTGGATATTAAAGGAAAAATCATCAAAACCGATGCGATGGGTTGCCAGAAAGATATTGCAGAGAAGATACAAAAACAGGGAGGTGATtatttatt             <  1:722660/139‑1 (MQ=21)                                                                                                                             cAATGAGACCACAGCTATCCCTGAACTTCTTAACATGCTGGATATTAAAGGAAAAATCATCAAAACCGATGCGATGGGTTGCCAGAAAGATATTGCAGAGAAGATACAAAAACAGGGAGGTGATTATTTATTCGCTGt       <  2:1139788/138‑1 (MQ=21)                                                                                                                               aTGAGATCACAGCTATCCCTGAACTTCTTAACATGCTGGATATTAAAGGAAAAATCATCAAAACCGATGCGATGGGTTGCCAGAAAGATATTGCAGAGAAGATACAAAAACAGGGAGGTGATTATTTATTCGCTGTaa     >  1:144246/1‑138 (MQ=34)                                                                                                                                tGAGACCACAGCTATCCCTGAACTTCTTAACATGCTGGATATTAAAGGAAAAATCATCAAAACCGATGCGATGGGTTGCCAGAAAGATATTGCAGAGAAGATACAAAAACAGGGAGGTGATTATTTATTCGCTGTaa     >  1:329453/1‑137 (MQ=21)                                                                                                                                  agaCCACAGCTATCCCTGAACTTCTTAACATGCTGGATATTAAAGGAAAAATCATCAAAACCGATGCGATGGGTTGCCAGAAAGATATTGCAGAGAAGATACAAAAACAGGGAGGTGATTATTTATTCGCTGTAAAAg  <  2:1161668/138‑1 (MQ=21)                                                                                                                                     |                                                                                                                                       TTGATGGAAAAATACACCGGCATTCTTATGACAAGAGTCGCCGTAAGGGAGCGATTCATGTCATTAGTGCGTTCTCAACAATGCACAGTCTGGTCATCGGACAGATCAAGACGGATAAGAAATCCAATGAGATCACAGCTATCCCTGAACTTCTTAACATGCTGGATATTAAAGGAAAAATCATCAAAACCGATGCGATGGGTTGCCAGAAAGATATTGCAGAGAAGATACAAAAACAGGGAGGTGATTATTTATTCGCTGTAAAAG  >  NZ_CP009273/733870‑734136

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑