Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	320,160	T→A	intergenic (‑159/‑67)	rclA ← / → rclR	reactive chlorine stress species (RCS) resistance protein, pyridine nucleotide‑dependent disulfide oxidoreductase family/reactive chlorine species (RCS)‑specific activator of the rcl genes

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	320,160	0	T	A	100.0%	165.1 / NA	52	intergenic (‑159/‑67)	rclA/rclR	reactive chlorine stress species (RCS) resistance protein, pyridine nucleotide‑dependent disulfide oxidoreductase family/reactive chlorine species (RCS)‑specific activator of the rcl genes
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base A (26/26);  total (26/26)

ATGACTATAGACGCAAAAGAGCAAATAACATTTCTTCACAACGCTTGATATTTTGTCTTATCGTCTGATATTTTCTTTTTCTTAATCAGAATCACAAAACAAAAATCATGATTAACTATTTGATGGTATTAGATTAGTTATTTACTAAGATTGTTGGTGTTTGTAATCAAAAACCACTCAGGAGTCTGATATGGATGCCCTTAGCCGTTTGTTGATGCTTAACGCTCCACAAGGAACGATCGATAAGAATTGC  >  NC_000913/320037‑320289                                                                                                                            |                                                                                                                                  atGACTATAGACGCAAAAGAGCAAATAACATTTCTTCACAACGCTTGATATTTTGTCTTATCGTCTGATATTTTCTTTTTCTTAATCAGAATCACAAAACAAAAATCATGATTAACTATTTGAAGGTATTAGATTAGtt                                                                                                                    >  1:103444/1‑139 (MQ=255)  tGACTATAGACGCAAAAGAGCAAATAACATTTCTTCACAACGCTTGATATTTTGTCTTATCGTCTGATATTTTCTTTTTCTTAATCAGAATCACAAAACAAAAATCATGATTAACTATTTGAAGGTATTAGATTAGTTa                                                                                                                   <  1:405629/139‑1 (MQ=255)  tGACTATAGACGCAAAAGAGCAAATAACATTTCTTCACAACGCTTGATATTTTGTCTTATCGTCTGATATTTTCTTTTTCTTAATCAGAATCACAAAACAAAAATCATGATTAACTATTTGAAGGTATTAGATTAGTTa                                                                                                                   <  2:661037/139‑1 (MQ=255)        taGACGCAAAAGAGCAAATAACATTTCTTCACAACGCTTGATATTTTGTCTTATCGTCTGATATTTTCTTTTTCTTAATCAGAATCACAAAACAAAAATCATGATTAACTATTTGAAGGTATTAGATTAGTTATTTACt                                                                                                             >  2:249992/1‑139 (MQ=255)        taGACGCAAAAGAGCAAATAACATTTCTTCACAACGCTTGATATTTTGTCTTATCGTCTGATATTTTCTTTTTCTTAATCAGAATCACAAAACAAAAATCATGATTAACTATTTGAAGGTATTAGATTAGTTATTTACt                                                                                                             >  1:800733/1‑139 (MQ=255)          gACGCAAAAGAGCAAATAACATTTCTTCACAACGCTTGATATTTTGTCTTATCGTCTGATATTTTCTTTTTCTTAATCAGAATCACAAAACAAAAATCATGATTAACTATTTGAAGGTATTAGATTAGTTATTTACTaa                                                                                                           >  2:1033711/1‑139 (MQ=255)           aCGCAAAAGAGCAAATAACATTTCTTCACAACGCTTGATATTTTGTCTTATCGTCTGATATTTTCTTTTTCTTAATCAGAATCACAAAACAAAAATCATGATTAACTATTTGAAGGTATTAGATTAGTTATTTACTAAg                                                                                                          >  1:474606/1‑139 (MQ=255)               aaaaGAGCAAATAACATTTCTTCACAACGCTTGATATTTTGTCTTATCGTCTGATATTTTCTTTTTCTTAATCAGAATCACAAAACAAAAATCATGATTAACTATTTGAAGGTATTAGATTAGTTATTTACTAAGAttg                                                                                                      >  2:248411/1‑139 (MQ=255)                aaaGAGCAAATAACATTTCTTCACAACGCTTGATATTTTGTCTTATCGTCTGATATTTTCTTTTTCTTAATCAGAATCACAAAACAAAAATCATGATTAACTATTTGAAGGTATTAGATTAGTTATTTACTAAGAttgt                                                                                                     >  2:223510/1‑139 (MQ=255)                aaaGAGCAAATAACATTTCTTCACAACGCTTGATATTTTGTCTTATCGTCTGATATTTTCTTTTTCTTAATCAGAATCACAAAACAAAAATCATGATTAACTATTTGAAGGTATTAGATTAGTTATTTACTAAGAttgt                                                                                                     >  1:791271/1‑139 (MQ=255)                aaaGAGCAAATAACATTTCTTCACAACGCTTGATATTTTGTCTTATCGTCTGATATTTTCTTTTTCTTAATCAGAATCACAAAACAAAAATCATGATTAACTATTTGAAGGTATTAGATTAGTTATTTACTAAGAttgt                                                                                                     >  2:470650/1‑139 (MQ=255)                aaaGAGCAAATAACATTTCTTCACAACGCTTGATATTTTGTCTTATCGTCTGATATTTTCTTTTTCTTAATCAGAATCACAAAACAAAAATCATGATTAACTATTTGAAGGTATTAGATTAGTTATTTACTAAGAttgt                                                                                                     >  1:566134/1‑139 (MQ=255)                aaaGAGCAAATAACATTTCTTCACAACGCTTGATATTTTGTCTTATCGTCTGATATTTTCTTTTTCTTAATCAGAATCACAAAACAAAAATCATGATTAACTATTTGAAGGTATTAGATTAGTTATTTACTAAGAttgt                                                                                                     >  2:811310/1‑139 (MQ=255)                         aTAACATTTCTTCACAACGCTTGATATTTTGTCTTATCGTCTGATATTTTCTTTTTCTTAATCAGAATCACAAAACAAAAATCATGATTAACTATTTGAAGGTATTAGATTAGTTATTTACTAAGATTGTTGGTGTTTg                                                                                            <  2:583724/139‑1 (MQ=255)                              aTTTCTTCACAACGCTTGATATTTTGTCTTATCGTCTGATATTTTCTTTTTCTTAATCAGAATCACAAAACAAAAATCATGATTAACTATTTGAAGGTATTAGATTAGTTATTTACTAAGATTGTTGGTGTTTGTAATc                                                                                       >  1:523584/1‑139 (MQ=255)                                ttcttcACAACGCTTGATATTTTGTCTTATCGTCTGATATTTTCTTTTTCTTAATCAGAATCACAAAACAAAAATCATGATTAACTATTTGAAGGTATTAGATTAGTTATTTACTAAGATTGTTGGTGTTTGTAATCaa                                                                                     >  1:848188/1‑139 (MQ=255)                                          cGCTTGATATTTTGTCTTATCGTCTGATATTTTCTTTTTCTTAATCAGAATCACAAAACAAAAATCATGATTAACTATTTGAAGGTATTAGATTAGtt                                                                                                                    <  1:1044249/98‑1 (MQ=255)                                          cGCTTGATATTTTGTCTTATCGTCTGATATTTTCTTTTTCTTAATCAGAATCACAAAACAAAAATCATGATTAACTATTTGAAGGTATTAGATTAGtt                                                                                                                    >  2:1044249/1‑98 (MQ=255)                                          cGCTTGATATTTTGTCTTATCGTCTGATATTTTCTTTTTCTTAATCAGAATCACAAAACAAAAATCATGATTAACTATTTGAAGGTATTAGATTAGTTATTTACTAAGATTGTTGGTGTTTGTAATCAAAAACCACTCa                                                                           >  2:147012/1‑139 (MQ=255)                                          cGCTTGATATTTTGTCTTATCGTCTGATATTTTCTTTTTCTTAATCAGAATCACAAAACAAAAATCATGATTAACTATTTGAAGGTATTAGATTAGTTATTTACTAAGATTATTGGTGTTTGTAATCAAAAACCACTCa                                                                           <  1:955581/139‑1 (MQ=255)                                           gCTTGATATTTTGTCTTATCGTCTGATATTTTCTTTTTCTTAATCAGAATCACAAAACAAAAATCATGATTAACTATTTGAAGGTATTAGATTAGTTATTTACTAAGATTGTTGGTGTTTGTAATCAAAAACCACTCAg                                                                          <  1:275619/139‑1 (MQ=255)                                           gCTTGATATTTTGTCTTATCGTCTGATATTTTCTTTTTCTTAATCAGAATCACAAAACAAAAATCATGATTAACTATTTGAAGGTATTAGATTAGTTATTTACTAAGATTGTTGGTGTTTGTAATCAAAAACCACTCAg                                                                          <  1:940728/139‑1 (MQ=255)                                             ttGATATTTTGTCTTATCGTCTGATATTTTCTTTTTCTTAATCAGAATCACAAAACAAAAATCATGATTAACTATTTGAAGGTATTAGATTAGTTATTTACTAAGATTGTTGGTGTTTGTAATCAAAAACCACTCAGGa                                                                        >  1:517539/1‑139 (MQ=255)                                             ttGATATTTTGTCTTATCGTCTGATATTTTCTTTTTCTTAATCAGAATCACAAAACAAAAATCATGATTAACTATTTGAAGGTATTAGATTAGTTATTTACTAAGATTGTTGGTGTTTGTAATCAAAAACCACTCAGGa                                                                        >  2:912724/1‑139 (MQ=255)                                              tGATATTTTGTCTTATCGTCTGATATTTTCTTTTTCTTAATCAGAATCACAAAACAAAAATCATGATTAACTATTTGAAGGTATTAGATTAGTTATTTACTAAGATTGTTGGTGTTTGTAATCAAAAACCACTCAGGAg                                                                       <  1:233856/139‑1 (MQ=255)                                               gATATTTTGTCTTATCGTCTGATATTTTCTTTTTCTTAATCAGAATCACAAAACAAAAATCATGATTAACTATTTGAAGGTATTAGATTAGTTATTTACTAAGATTGTTGGTGTTTGTAATCAAAAACCACTCAGGAGt                                                                      <  2:566134/139‑1 (MQ=255)                                                  atTTTGTCTTATCGTCTGATATTTTCTTTTTCTTAATCAGAATCACAAAACAAAAATCATGATTAACTATTTGAAGGTATTAGATTAGTTATTTACTAAGATTGTTGGTGTTTGTAATCAAAAACCACTCAGGAGTCTg                                                                   <  1:678667/139‑1 (MQ=255)                                                    tttGTCTTATCGTCTGATATTTTCTTTTTCTTAATCAGAATCACAAAACAAAAATCATGATTAACTATTTGAAGGTATTAGATTAGTTATTTACTAAGATTGTTGGTGTTTGTAATCAAAAACCACTCAGGAGTCTGat                                                                 <  2:791271/139‑1 (MQ=255)                                                        tCTTATCGTCTGATATTTTCTTTTTCTTAATCAGAATCACAAAACAAAAATCATGATTAACTATTTGAAGGTATTAGATTAGTTATTTACTAAGATTGTTGGTGTTTGTAATCAAAAACCACTCAGGAGTCTGATATgg                                                             >  2:439417/1‑139 (MQ=255)                                                         cTTATCGTCTGATATTTTCTTTTTCTTAATCAGAATCACAAAACAAAAATCATGATTAACTATTTGAAGGTATTAGATTAGTTATTTACTAAGATTGTTGGTGTTTGTAATCAAAAACCACTCAGGAGTCTGATATGGa                                                            <  1:871187/139‑1 (MQ=255)                                                          ttATCGTCTGATATTTTCTTTTTCTTAATCAGAATCACAAAACAAAAATCATGATTAACTATTTGAAGGTATTAGATTAGTTATTTACTAAGATTGTTGGTGTTTGTAATCAAAAACCACTCAGGAGTCTGATATGGAt                                                           <  1:439417/139‑1 (MQ=255)                                                           tATCGTCTGATATTTTCTTTTTCTTAATCAGAATCACAAAACAAAAATCATGATTAACTATTTGAAGGTATTAGATTAGTTATTTACTAAGATTGTTGGTGTTTGTAATCAAAAACCACTCa                                                                           >  2:96859/1‑122 (MQ=255)                                                           tATCGTCTGATATTTTCTTTTTCTTAATCAGAATCACAAAACAAAAATCATGATTAACTATTTGAAGGTATTAGATTAGTTATTTACTAAGATTGTTGGTGTTTGTAATCAAAAACCACTCa                                                                           <  1:96859/122‑1 (MQ=255)                                                            aTCCTCTGATATTTGCTTTTTCTTATTCAGAATCACAAAACAAAAATTATCATTACCTATTTGTATCTACTAGATTAGTTACCTACTAAAATTGTTGGTGTTTGTAATCAAAAACCACTCAGGAGTCTGATATGGAtac                                                         >  2:446164/1‑137 (MQ=255)                                                                            tatttcttACTCAGAATCACAAAACAAAAATCATGATTAACTATTTGAAGGTATTAGATTAGTTATTTACTAAGATTGTTGGTGTTTGTAATCAAAAACCACTCAGGAGTCTGATATGTATGCCCTTAGCCGTttgttg                                         <  2:622160/137‑1 (MQ=255)                                                                              tttcttAATCAGAATCACAAAACAAAAATCATGATTAACTATTTGAAGGTATTAGATTAGTTATTTACTAAGATTGTTGGTGTTTGTAATCAAAAACCACTCAGGAGTCTGATATGGATGCCCTTAGCCGTTTGTTGAt                                       >  1:581378/1‑139 (MQ=255)                                                                                tcttAATCAGAATCACAAAACAAAAATCATGATTAACTATTTGAAGGTATTAGATTAGTTATTTACTAAGATTGTTGGTGTTTGTAATCaaa                                                                                    >  2:685072/1‑92 (MQ=255)                                                                                tcttAATCAGAATCACAAAACAAAAATCATGATTAACTATTTGAAGGTATTAGATTAGTTATTTACTAAGATTGTTGGTGTTTGTAATCaaa                                                                                    <  1:685072/92‑1 (MQ=255)                                                                                      tCAGAATCACAAAACAAAAATCATGATTAACTATTTGAAGGTATTAGATTAGTTATTTACTAAGATTGTTGGTGTTTGTAATCAAAAACCACTCAGGAGTCTGATATGGATGCCCTTAGCCGTTTGTTGATGCTTAACg                               <  1:470650/139‑1 (MQ=255)                                                                                      tCAGAATCACAAAACAAAAATCATGATTAACTATTTGAAGGTATTAGATTAGTTATTTACTAAGATTGTTGGTGTTTGTAATCAAAAACCACTCAGGAGTCTGATATGGATGCCCTTAGCCGTTTGTTGATGCTTAACg                               <  2:517539/139‑1 (MQ=255)                                                                                      tCAGAATCACAAAACAAAAATCATGATTAACTATTTGAAGGTATTAGATTAGTTATTTACTAAGATTGTTGGTGTTTGTAATCAAAAACCACTCAGGAGTCTGATATGGATGCCCTTAGCCGTTTGTTGATGCTTAACg                               <  2:523584/139‑1 (MQ=255)                                                                                        aGAATCACAAAACAAAAATCATGATTAACTATTTGAAGGTATTAGATTAGTTATTTACTAAGATTGTTGGTGTTTGTAATCAAAAACCACTCAGGAGTCTGATATGGATGCCCTTAGCCGTTTGTTGATGCTTAACGCt                             <  2:103444/139‑1 (MQ=255)                                                                                               caaaacaaaaATCATGATTAACTATTTGAAGGTATTAGATTAGTTATTTACTAAGATTGTTGGTGTTTGTAATCAAAAACCACTCAGGAGTCTGATATGGATGCCCTTAGCCGTTTGTTGATGCTTAACGCTCCACAAg                      >  2:83843/1‑139 (MQ=255)                                                                                                aaaacaaaaATCATGATTAACTATTTGAAGGTATTAGATTAGTTATTTACTAAGATTGTTGGTGTTTGTAATCAAAAACCACTCAGGAGTCTGACATGGATGCCCTTAGCCGTTTGTTGATGCTTAACg                               <  2:196451/129‑1 (MQ=255)                                                                                                aaaacaaaaATCATGATTAACTATTTGAAGGTATTAGATTAGTTATTTACTAAGATTGTTGGTGTTTGTAATCAAAAACCACTCAGGAGTCTGACATGGATGCCCTTAGCCGTTTGTTGATGCTTAACg                               >  1:196451/1‑129 (MQ=255)                                                                                                  aacaaaaATCATGATTAACTATTTGAAGGTATTAGATTAGTTATTTACTAAGATTGTTGGTGTTTGTAATCAAAAACCACTCAGGAGTCTGATATGGATGCCCTTAGCCGTTTGTTGATGCTTAACGCTCCACAAGGaa                   <  1:147012/139‑1 (MQ=255)                                                                                                    caaaaATCATGATTAACTATTTGAAGGTATTAGATTAGTTATTTACTAAGATTGTTGGTGTTTGTAATCAAAAACCACTCAGGAGTCTGATATGGATGCCCTTAGCCGTTTGTTGATGCTTAACGCTCCACAAGGAAcg                 >  2:817069/1‑139 (MQ=255)                                                                                                    caaaaATCATGATTAACTATTTGAAGGTATTAGATTAGTTATTTACTAAGATTGTTGGTGTTTGTAATCAAAAACCACTCAGGAGTCTGATATGGATGCCCTTAGCCGTTTGTTGATGCTTAACGCTCCACAAGGAAcg                 >  1:1024862/1‑139 (MQ=255)                                                                                                       aaaTCATGATTAACTATTTGAAGGTATTAGATTAGTTATTTACTAAGATTGTTGGTGTTTGTAATCAAAAACCACTCAGGAGTCTGATATGGATGCCCTTAGCCGTTTGTTGATGCTTAACGCTCCACAAGGAAcgatc              <  1:577083/139‑1 (MQ=255)                                                                                                                 tAACTATTTGAAGGTATTAGATTAGTTATTTACTAAGATTGTTGGTGTTTGTAATCAAAAACCACTCAGGAGTCTGATATGGATGCCCTTAGCCGTTTGTTGATGCTTAACGCTCCACAAGGAACGATCGATAAGAAtt    <  1:912724/139‑1 (MQ=255)                                                                                                                   aCTATTTGAAGGTATTAGATTAGTTATTTACTAAGATTGTTGGTGTTTGTAATCAAAAACCACTCAGGAGTCTGATATGGATGCCCTTAGCCGTTTGTTGATGCTTAACGCTCCACAAGGAACGATCGATAAGAATTGc  <  1:249992/139‑1 (MQ=255)                                                                                                                   aCTATTTGAAGGTATTAGATTAGTTATTTACTAAGATTGTTGGTGTTTGTAATCAAAAACCACTCAGGAGTCTGATATGGATGCCCTTAGCCGTTTGTTGATGCTTAACGCTCCACAAGGAACGATCGATAAGAATTGc  <  2:848188/139‑1 (MQ=255)                                                                                                                            |                                                                                                                                  ATGACTATAGACGCAAAAGAGCAAATAACATTTCTTCACAACGCTTGATATTTTGTCTTATCGTCTGATATTTTCTTTTTCTTAATCAGAATCACAAAACAAAAATCATGATTAACTATTTGATGGTATTAGATTAGTTATTTACTAAGATTGTTGGTGTTTGTAATCAAAAACCACTCAGGAGTCTGATATGGATGCCCTTAGCCGTTTGTTGATGCTTAACGCTCCACAAGGAACGATCGATAAGAATTGC  >  NC_000913/320037‑320289

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑