Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	1,063,912	+C	coding (577/1218 nt)	brpA ←	LytR family transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,063,909	1	.	C	89.7%	128.5 / 9.7	39	coding (580/1218 nt)	brpA	LytR family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base . (3/1);  new base C (21/14);  total (24/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TATCAAGTTTATCAATAGAATCAACTTCCTGTGCTTTTTGGAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑A‑CCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATGCTTTCATATTGACTCTCACATAATAATCAACAG  >  CP000730/1063762‑1064049                                                                                                                                                        |                                                                                                                                             tATCAAGTTTATCAATAGAATCAACTTCCTGTGCTTTTTGGAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑a                                                                                                                                               <  1:110544/148‑1 (MQ=255) tATCAAGTTTATCAATAGAATCAACTTCCTGTGCTTTTTGGAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑a                                                                                                                                               <  1:156008/148‑1 (MQ=255)         ttATCAATAGAATCAACTTCCTGTGCTTTTTGGAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑A‑CCCctttt                                                                                                                                      >  2:302746/1‑148 (MQ=255)             cAATAGAATCAACTTCCTGTGCTTTTTGGAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTttttaa                                                                                                                                   >  1:223156/1‑148 (MQ=255)               aTAGAATCAACTTCCTGTGCTTTTTGGAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTttttaatt                                                                                                                                 <  2:127648/148‑1 (MQ=255)                            ccTGTGCTTTTTGGAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAg                                                                                                                    >  2:127270/1‑148 (MQ=255)                                     tttGGAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCtg                                                                                                           <  1:201248/148‑1 (MQ=255)                                      ttGGAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCtgt                                                                                                          <  2:132675/148‑1 (MQ=255)                                       tGGAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCtgtg                                                                                                         >  1:409488/1‑148 (MQ=255)                                        ggAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTgtgt                                                                                                        >  1:131994/1‑148 (MQ=255)                                         gattAAAATCTTAATTAATTCCACTTGACGTTGTCCACGTTTTACGTCTGAATCATCATGTCTAGATCTGGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGGAA‑A‑CCCTTTTTTAATATTAATCTTACAAGTATAATCTGTGtt                                                                                                       >  2:289570/4‑148 (MQ=255)                                                aTCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCa                                                                                                <  2:183122/148‑1 (MQ=255)                                                   ttaattaaTTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCAttt                                                                                             <  1:116496/148‑1 (MQ=255)                                                   ttaattaaTTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCAttt                                                                                             <  1:116602/148‑1 (MQ=255)                                                             ccATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATg                                                                                   <  2:232744/148‑1 (MQ=255)                                                             ccATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATg                                                                                   >  1:25478/1‑148 (MQ=255)                                                              cATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATgg                                                                                  >  2:118306/1‑148 (MQ=255)                                                                tttGACGTTGTCCACGTTTTACGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTACAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTCAGTCGTATGGca                                                                                >  2:95298/1‑148 (MQ=255)                                                                  tgtcGTTGTCCACGTTTTAAGTCTGAATCATCGTGTTTAGTTCTAGGCTCTGCTAATGCCTCATCACCATTTAA‑TTTTTGG‑TCC‑CCCTTTTTTCATTTTGTTCTTTCCAGTATCTTCTGTGTTAGGTTCATTTAAGTCGTATGGcaca                                                                              <  2:97062/145‑1 (MQ=255)                                                                  tGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGcaca                                                                              <  2:50517/148‑1 (MQ=255)                                                                      gTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCAcatcat                                                                          <  1:172202/148‑1 (MQ=255)                                                                            cACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTATTTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGtata                                                                    >  2:71315/1‑148 (MQ=255)                                                                            cACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTATTTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATAATAGtata                                                                    >  2:231933/1‑148 (MQ=255)                                                                            cACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTTATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGtata                                                                    >  2:231940/1‑148 (MQ=255)                                                                            cACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGtata                                                                    >  1:222787/1‑148 (MQ=255)                                                                                   tAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTTTTTTTTTTCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCACAGTATCTGccccc                                                             >  2:245597/1‑148 (MQ=255)                                                                                         tGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTTTT‑T‑T‑TTTTTTTTTAATTTTAATCTTACCAGTATTTTCTGTGTTAGGTTCATTTAAGTCGTATGGCACTTCCTAGTATATGCCACCAAGCTc                                                       >  2:55644/1‑148 (MQ=255)                                                                                         tGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTc                                                       >  1:45004/1‑148 (MQ=255)                                                                                         tGAATCATGAAGCCTAGTACTAGCAACTGCTAAAGCCTCATCACCATCTAA‑TTTTTGG‑T‑ACCCCTTTTATAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTc                                                       >  2:55653/1‑148 (MQ=255)                                                                                          gAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCa                                                      <  2:92147/148‑1 (MQ=255)                                                                                                         gTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTTTTTTTTTTTTTACTAGTATCATCTGTGTTATGTTCATTTAAGTCGTATGGCACATCATTGTCTTTGTCTCCAAGCTTATTTTCAGTCTCTACa                                       >  2:101268/1‑148 (MQ=255)                                                                                                         gTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCTTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACa                                       >  2:187504/1‑148 (MQ=255)                                                                                                         gTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACa                                       >  2:227306/1‑148 (MQ=255)                                                                                                               gCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATGCt                                 >  1:388398/1‑148 (MQ=255)                                                                                                                          aGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATGCTTTCATATTGAc                      <  1:66340/148‑1 (MQ=255)                                                                                                                            ccTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATGCTTTCATATTGActc                    >  1:258540/1‑148 (MQ=255)                                                                                                                            ccTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCACTTACAGCCTCGACAAATGCTTTCATATTGActc                    >  1:158074/1‑148 (MQ=255)                                                                                                                               catcaCCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTTTTTTTTTTCTTACCAGTATCATCTGTGTTAGTTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATGCTTTCATATTTACTCTca                 >  2:45322/1‑148 (MQ=255)                                                                                                                               catcaCCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATGCTTTCATATTGACTCTca                 <  2:367639/148‑1 (MQ=255)                                                                                                                                             tttttGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATGCTTTCATATTGACTCTCACATAATAATCAAc    <  1:118302/148‑1 (MQ=255)                                                                                                                                               tttGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATGCTTTCATATTGACTCTCACATAATAATCAACAg  <  1:381075/148‑1 (MQ=255)                                                                                                                                                        |                                                                                                                                             TATCAAGTTTATCAATAGAATCAACTTCCTGTGCTTTTTGGAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑A‑CCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATGCTTTCATATTGACTCTCACATAATAATCAACAG  >  CP000730/1063762‑1064049

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑