Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	2,700,943	C→T	S73N (AGC→AAC)	rseC ←	SoxR‑reducing system protein RseC

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	2,700,943	0	C	T	95.5%	240.2 / ‑0.9	67	S73N (AGC→AAC)	rseC	SoxR‑reducing system protein RseC
Reads supporting (aligned to +/- strand):  ref base C (2/1);  new base T (28/36);  total (30/37)
Fisher's exact test for biased strand distribution p-value = 5.83e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

GCCAATACCACCGAGGATCGCACCACATAATGCTGCGACGTCAGAAGCAAAGAGTAGCTGAAATAGCGAAGCGATAAGGAATAATCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGCTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTAACGGCTCATCACAGGGTACGACAATGGTATGCGTGGTTTGCGGGCCAAGTTTATTTAACACGCGGCTACCGCAACCGGCGCGTGAAG  >  NZ_CP009273/2700813‑2701072                                                                                                                                   |                                                                                                                                  gCCAATACCACCGAGGATCGCACCACATAATGCTGCGACGTCAGAAGCAAAGAGTAGCTGAAATAGCGAAGCGATAAGGAATAATCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCg                                                                                                                           >  1:176112/1‑139 (MQ=255) gCCAATACCACCGAGGATCGCACCACATAATGCTGCGACGTCAGAAGCAAAGAGTAGCTGAAATAGCGAAGCGATAAGGAATAATCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGCTGCCTTCg                                                                                                                           >  2:1185435/1‑139 (MQ=255)      tACCACCGAGGATCGCACCACATAATGCTGCGACGTCAGAAGCAAAGAGTAGCTGAAATAGCGAAGCGATAAGGAATAATCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGAt                                                                                                                      >  2:128149/1‑139 (MQ=255)        ccaccGAGGATCGCACCACATAATGCTGCGACGTCAGAAGCAAAGAGTAGCTGAAATAGCGAAGCGATAAGGAATAATCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATc                                                                                                                     <  1:824039/138‑1 (MQ=255)           ccGAGGATCGCACCACATAATGCTGCGACGTCAGAAGCAAAGAGTAGCTGAAATAGCGAAGCGATAAGGAATAATCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATcccc                                                                                                                  >  2:775826/1‑138 (MQ=255)              aGGATCGCACCACATAATGCTGCGACGTCAGAAGCAAAGAGTAGCTGAAATAGCGAAGCGATAAGGAATAATCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAAtt                                                                                                              >  1:604337/1‑139 (MQ=255)                gATCGCACCACATAATGCTGCGACGTCAGAAGCAAAGAGTAGCTGAAATAGCGAAGCGATAAGGAATAATCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTcc                                                                                                            <  1:769209/139‑1 (MQ=255)                          caTAATGCTGCGACGTCAGAAGCAAAGAGTAGCTGAAATAGCGAAGCGATAAGGAATAATCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGcc                                                                                                  <  2:929819/139‑1 (MQ=255)                          caTAATGCTGCGACGTCAGAAGCAAAGAGTAGCTGAAATAGCGAAGCGATAAGGAATAATCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGcc                                                                                                  <  2:192377/139‑1 (MQ=255)                              aTGCTGCGACGTCAGAAGCAAAGAGTAGCTGAAATAGCGAAGCGATAAGGAATAATCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCg                                                                                               <  1:1251875/138‑1 (MQ=255)                                  tgcGACGTCAGAAGCAAAGAGTAGCTGAAATAGCGAAGCGATAAGGAATAATCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGcc                                                                                                  >  1:1178139/1‑131 (MQ=255)                                  tgcGACGTCAGAAGCAAAGAGTAGCTGAAATAGCGAAGCGATAAGGAATAATCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGcc                                                                                                  <  2:1178139/131‑1 (MQ=255)                                  tgcGACGTCAGAAGCAAAGAGTAGCTGAAATAGCGAAGCGATAAGGAATAATCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCAc                                                                                           >  2:987089/1‑138 (MQ=255)                                    cGACGTCAGAAGCAAAGAGTAGCTGAAATAGCGAAGCGATAAGGAATAATCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTaa                                                                                        <  1:987089/139‑1 (MQ=255)                                    cGACGTCAGAAGCAAAGAGTAGCTGAAATAGCGAAGCGATAAGGAATAATCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTaa                                                                                        >  2:17707/1‑139 (MQ=255)                                       cGTCAGAAGCAAAGAGTAGCTGAAATAGCGAAGCGATAAGGAATAATCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTAACgg                                                                                     <  1:105510/139‑1 (MQ=255)                                         tCAGAAGCAAAGAGTAGCTGAAATAGCGAAGCGATAAGGAATAATCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCg                                                                                                                        >  1:784824/1‑102 (MQ=255)                                         tCAGAAGCAAAGAGTAGCTGAAATAGCGAAGCGATAAGGAATAATCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCg                                                                                                                        <  2:784824/102‑1 (MQ=255)                                         tCAGAAGCAAAGAGTAGCTGAAATAGCGAAGCGATAAGGAATAATCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTaa                                                                                        <  1:3527/134‑1 (MQ=255)                                         tCAGAAGCAAAGAGTAGCTGAAATAGCGAAGCGATAAGGAATAATCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTaa                                                                                        >  2:3527/1‑134 (MQ=255)                                         tCAGAAGCAAAGAGTAGCTGAAATAGCGAAGCGATAAGGAATAATCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTAACGGCt                                                                                   <  1:664394/139‑1 (MQ=255)                                         tCAGAAGCAAAGAGTAGCTGAAATAGCGAAGCGATAAGGAATAATCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTAACGGCt                                                                                   >  2:290329/1‑139 (MQ=255)                                              aGCAAAGAGTAGCTGAAATAGCGAAGCGATAAGGAATAATCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTAACGGCtcatca                                                                              <  1:221863/139‑1 (MQ=255)                                              aGCAAAGAGTAGCTGAAATAGCGAAGCGATAAGGAATAATCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTAACGGCtcatca                                                                              <  1:609885/139‑1 (MQ=255)                                              aGCAAAGAGTAGCTGAAATAGCGAAGCGATAAGGAATAATCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTAACGGCtcatca                                                                              <  1:128149/139‑1 (MQ=255)                                              aGCAAAGAGTAGCTGAAATAGCGAAGCGATAAGGAATAATCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTAACGGCtcatca                                                                              <  1:17707/139‑1 (MQ=255)                                                cAAAGAGTAGCTGAAATAGCGAAGCGATAAGGAATAATCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTAACGGCTCATcaca                                                                            <  2:231919/139‑1 (MQ=255)                                                cAAAGAGTAGCTGAAATAGCGAAGCGATAAGGAATAATCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTAACGGCTCATcaca                                                                            <  2:245391/139‑1 (MQ=255)                                                   agagTAGCTGAAATAGCGAAGCGATAAGGAATAATCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTAACGGCTCATCACAggg                                                                         <  1:1081953/139‑1 (MQ=255)                                                   agagTAGCTGAAATAGCGAAGCGATAAGGAATAATCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTAACGGCTCATCACAggg                                                                         <  2:672920/139‑1 (MQ=255)                                                   agagTAGCTGAAATAGCGAAGCGATAAGGAATAATCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTAACGGCTCATCACAggg                                                                         <  2:1045142/139‑1 (MQ=255)                                                       tAGCTGAAATAGCGAAGCGATAAGGAATAATCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTAACGGCTCATCACAGGGTACg                                                                     <  2:681247/139‑1 (MQ=255)                                                         gCTGAAATAGCGAAGCGATAAGGAATAATCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTAACGGCTCATCACAGGGTACGa                                                                    >  1:132429/1‑138 (MQ=255)                                                          cTGAAATAGCGAAGCGATAAGGAATAATCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTAACGGCTCATCACAGGGTACGACa                                                                  <  2:176112/139‑1 (MQ=255)                                                                   cgaagcgaTAAGGAATAATCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTAACGGCTCATCACAGGGTACGACAATGGTATGc                                                         >  1:1016741/1‑139 (MQ=255)                                                                   cgaagcgaTAAGGAATAATCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTAACGGCTCATCACAGGGTACGACAATGGTATGc                                                         >  1:1222993/1‑139 (MQ=255)                                                                    gaagcgaTAAGGAATAATCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTAACGGCTCATCACAGGGTACGACAATGGTATGCg                                                        >  2:491354/1‑139 (MQ=255)                                                                       gcgaTAAGGAATAATCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTAACGGCTCATCACAGGGTACGACAATGGTATGCGTgg                                                     >  2:464236/1‑139 (MQ=255)                                                                       gcgaTAAGGAATAATCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTAACGGCTCATCACAGGGTACGACAATGGTATGCGTgg                                                     >  2:190594/1‑139 (MQ=255)                                                                                 ataatCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTAACGGCTCATCACAGGGTACGACAATGGTATGCGTGGTTTGCGGGcc                                           <  2:132429/139‑1 (MQ=255)                                                                                    atCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTAACg                                                                                      >  1:1249762/1‑93 (MQ=255)                                                                                    atCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTAACg                                                                                      <  2:1249762/93‑1 (MQ=255)                                                                                    atCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTAACg                                                                                      >  1:1081649/1‑93 (MQ=255)                                                                                    atCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTAACg                                                                                      <  2:1081649/93‑1 (MQ=255)                                                                                    atCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTAACGGCTCATCACAGGGTACGACAATGGTATGCGTGGTTTGCGGGCCAAg                                        >  1:580735/1‑139 (MQ=255)                                                                                     tCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTAACGGCt                                                                                   <  2:792659/95‑1 (MQ=255)                                                                                     tCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTAACGGCt                                                                                   >  1:792659/1‑95 (MQ=255)                                                                                         accaGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTAACGGCTCATCACAggg                                                                         >  2:1116042/1‑101 (MQ=255)                                                                                         accaGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTAACGGCTCATCACAggg                                                                         <  1:1116042/101‑1 (MQ=255)                                                                                         accaGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTAACGGCTCATCACAGGGTACGACAATGGTATGCGTGGTTTGCGGGCCAAGtttat                                   >  1:616464/1‑139 (MQ=255)                                                                                          ccaGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTAACGGc                                                                                    <  2:666601/89‑1 (MQ=255)                                                                                          ccaGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTAACGGc                                                                                    >  1:666601/1‑89 (MQ=255)                                                                                                gcgACATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTAACGGCTCATCACAGGGTACGACAATGGTATGCGTGGTTTGCGGGCCAAGTTTATTTAacac                            <  1:715777/139‑1 (MQ=255)                                                                                                    cATATAAACCAGTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTAACGGCTCATCACAGGGTACGACAATGGTATGCGTGGTTTGCGGGCCAAGTTTATTTAACACGCgg                        <  1:237262/139‑1 (MQ=255)                                                                                                               gTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGccc                                                                                                 >  1:27558/1‑55 (MQ=255)                                                                                                               gTAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGccc                                                                                                 <  2:27558/55‑1 (MQ=255)                                                                                                                tAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGcc                                                                                                  >  1:482199/1‑53 (MQ=255)                                                                                                                tAATGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGcc                                                                                                  <  2:482199/53‑1 (MQ=255)                                                                                                                 aaTGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGcc                                                                                                  >  1:247159/1‑52 (MQ=255)                                                                                                                 aaTGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGcc                                                                                                  <  2:247159/52‑1 (MQ=255)                                                                                                                 aaTGCGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTAACGGCTCATCACAGGGTACGACAATGGTATGCGTGGTTTGCGGGCCAAGTTTATTTAACACGCGGCTACCGCAACCgg           >  1:88858/1‑139 (MQ=255)                                                                                                                     cGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGcc                                                                                                  >  2:381415/1‑48 (MQ=255)                                                                                                                     cGGAGCTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGcc                                                                                                  <  1:381415/48‑1 (MQ=255)                                                                                                                          cTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTAACGGCTCATCACAGGGTACGACAATGGTATGCGTGGTTTGCGGGCCAAGTTTATTTAACACGCGGCTACCGCAACCGGCGCGTGAAg  <  2:1016741/139‑1 (MQ=255)                                                                                                                          cTAAGCAGGTTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTAACGGCTCATCACAGGGTACGACAATGGTATGCGTGGTTTGCGGGCCAAGTTTATTTAACACGCGGCTACCGCAACCGGCGCGTGAAg  <  2:1222993/139‑1 (MQ=255)                                                                                                                                  gCTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTAACGGCTCATCACAGGGTACGACAATGGTATGCGTGGTTTGCGGGCCAAGTTTATTTAaca                             >  1:127321/1‑104 (MQ=255)                                                                                                                                  gCTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTAACGGCTCATCACAGGGTACGACAATGGTATGCGTGGTTTGCGGGCCAAGTTTATTTAaca                             <  2:127321/104‑1 (MQ=255)                                                                                                                                   |                                                                                                                                  GCCAATACCACCGAGGATCGCACCACATAATGCTGCGACGTCAGAAGCAAAGAGTAGCTGAAATAGCGAAGCGATAAGGAATAATCCCACCAGCGGCGACATATAAACCAGTAATGCGGAGCTAAGCAGGCTGCCTTCGGCGATCCCCAATTCCACTTTTTGCCCCGGCACTAACGGCTCATCACAGGGTACGACAATGGTATGCGTGGTTTGCGGGCCAAGTTTATTTAACACGCGGCTACCGCAACCGGCGCGTGAAG  >  NZ_CP009273/2700813‑2701072

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: ‑