Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP009974	542,115	2 bp→TG	intergenic (‑376/+152)	argD ← / ← RPPX_02300	acetylornithine aminotransferase/AraC family transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009974	542,115	0	C	T	77.1%	45.9 / 20.4	49	intergenic (‑376/+153)	argD/RPPX_02300	acetylornithine aminotransferase/AraC family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base C (0/11);  new base T (8/29);  total (8/41)
Fisher's exact test for biased strand distribution p-value = 1.70e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
*	CP009974	542,116	0	A	G	75.5%	45.8 / 23.5	49	intergenic (‑377/+152)	argD/RPPX_02300	acetylornithine aminotransferase/AraC family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base A (0/12);  new base G (8/29);  total (8/41)
Fisher's exact test for biased strand distribution p-value = 1.73e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGCGATGTTGATGTGTTGGCGGGGAGATCGAGCGCCGCCCGCGCGGCGCTTCGCGGGTAAACCCGCTCCTACGTTTGTTTCGGGCCAGTCCCTCCTGTGCCTGGCGCGCGCGACCGCCTTGTTTGTACGACGCGATATCGAGGCATGCGCCAAGGCGTTCGCGCGCAAATGCCACAGGCATAACTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATTTGCGCCCCAACATCAACCTCAAGGCATAC  >  CP009974/541972‑542246                                                                                                                                                ||                                                                                                                                   ggCGATGTTGATGTGTTGGCGGGGAGATCGAGCGCCGCCCGCGCGGCGCTTCGCGGGTAAACCCGCTCCTACGCTTGTTTCGGGCCAGTCCCTCCTGCGCCCGGCGCGCGCGACCGCCTTGTTTGTTCGACGGGATATCGAGGTGTGCGcc                                                                                                                              <  1:4954256/151‑1 (MQ=14)   cGATGTTGATGTGTTGGCGGGGAGATCGAGCGCCGCCCGCGCGGCGCTTCGCGGGTAAACCCGCTCCTACGCTTGTTTCGGGCCAGTCCCTCCTGCGCCCGGCGCGCGCGACCGCCTTGTTTGTTCGACGGGATATCGAGGTGTGCGCCaa                                                                                                                            <  2:2089045/151‑1 (MQ=14)    gATGTTGATGTGTTGGCGGGGAGATCGAGCGCCGCCCGCGCGGCGCTTCGCGGGTAAACCCGCTCCTACGCTTGTTTCGGGCCAGTCCCTCCTGCGCCCGGCGCGCGCGACCGCCTTGTTTGTTCGACGGGATATCGAGGTGTGCGCCAAg                                                                                                                           <  1:6580743/151‑1 (MQ=14)      tGTTGATGTGTTGGCGGGGAGATCGAGCGCCGCCCGCGCGGCGCTTCGCGGGTAAACCCGCTCCTACGCTTGTTTCGGGCCAGTCCCTCCTGCGCCCGGCGCGCGCGACCGCCTTGTTTGTTCGACGGGATATCGAGGTGTGCGCCAAGGc                                                                                                                         <  1:2221948/151‑1 (MQ=14)      tGTTGATGTGTTGGCGGGGAGATCGAGCGCCGCCCGCGCGGCGCTTCGCGGGTAAACCCGCTCCTACGCTTGTTTCGGGCCAGTCCCTCCTGCGCCCGGCGCGCGCGACCGCCTTGTTTGTTCGACGGGATATCGAGGTGTGCGCCAAGGc                                                                                                                         >  1:2261768/1‑151 (MQ=14)      tGTTGATGTGTTGGCGGGGAGATCGAGCGCCGCCCGCGCGGCGCTTCGCGGGTAAACCCGCTCCTACGCTTGTTTCGGGCCAGTCCCTCCTGCGCCCGGCGCGCGCGACCGCCTTGTTTGTTCGACGGGATATCGAGGTGTGCGCCAAGGc                                                                                                                         <  1:3011126/151‑1 (MQ=14)      tGTTGATGTGTTGGCGGGGAGATCGAGCGCCGCCCGCGCGGCGCTTCGCGGGTAAACCCGCTCCTACGCTTGTTTCGGGCCAGTCCCTCCTGCGCCCGGCGCGCGCGACCGCCTTGTTTGTTCGACGGGATATCGAGGTGTGCGCCAAGGc                                                                                                                         <  1:3011174/151‑1 (MQ=14)      tGTTGATGTGTTGGCGGGGAGATCGAGCGCCGCCCGCGCGGCGCTTCGCGGGTAAACCCGCTCCTACGCTTGTTTCGGGCCAGTCCCTCCTGCGCCCGGCGCGCGCGACCGCCTTGTTTGTTCGACGGGATATCGAGGTGTGCGCCAAGGc                                                                                                                         <  1:3011199/151‑1 (MQ=14)        ttGATGTGTTGGCGGGGAGATCGAGCGCCGCCCGCGCGGCGCTTCGCGGGTAAACCCGCTCCTACGCTTGTTTCGGGCCAGTCCCTCCTGCGCCCGGCGCGCGCGACCGCCTTGTTTGTTCGACGGGATATCGAGGTGTGCGCCAAGGCGt                                                                                                                       <  2:4861246/151‑1 (MQ=14)        ttGATGTGTTGGCGGGGAGATCGAGCGCCGCCCGCGCGGCGCTTCGCGGGTAAACCCGCTCCTACGCTTGTTTCGGGCCAGTCCCTCCTGCGCCCGGCGCGCGCGACCGCCTTGTTTGTTCGACGGGATATCGAGGTGTGCGCCAAGGCGt                                                                                                                       <  1:2997131/151‑1 (MQ=14)        ttGATGTGTTGGCGGGGAGATCGAGCGCCGCCCGCGCGGCGCTTCGCGGGTAAACCCGCTCCTACGCTTGTTTCGGGCCAGTCCCTCCTGCGCCCGGCGCGCGCGACCGCCTTGTTTGTTCGACGGGATATCGAGGTGTGCGCCAAGGCGt                                                                                                                       <  1:6663290/151‑1 (MQ=14)        gtGATGGGTTGGCGGGGAGATCGAGCGCCGCCCGCGCGGCGCTTCGCGGGTAAACCCGCTCCTACGCTTGTTTCGGGCCAGTCCCTCCTGCGCCCGGCGCGCGCGACCGCCTTGTTTGTTCGACGGGATATCGAGGTGTGCGCCAAGGCGt                                                                                                                       <  1:6663078/150‑1 (MQ=14)         tGATGTGTTGGCGGGGAGATCGAGCGCCGCCCGCGCGGCGCTTCGCGGGTAAACCCGCTCCTACGCTTGTTTCGGGCCAGTCCCTCCTGCGCCCGGCGCGCGCGACCGCCTTGTTTGTTCGACGGGATATCGAGGTGTGCGCCAAGGCGtt                                                                                                                      <  1:3659380/151‑1 (MQ=14)          gATGTGTTGGCGGGGAGATCGCGCGCCGCCCGCGCGGCGCTTCGCGGGTAAACCCGCTCCTACGCTTGTTTCGGGCCAGTCCCTCCTGCGCCCGGCGCGCGCGACCGCCTTGTTTGTTCGACGGGATATCGAGGTGTGCGCCAAGGCGTTc                                                                                                                     <  1:3542459/151‑1 (MQ=14)          gATGTGTTGGCGGGGAGATCGAGCGCCGCCCGCGCGGCGCTTCGCGGGTAAACCCGCTCCTACGCTTGTTTCGGGCCAGTCCCTCCTGCGCCCGGCGCGCGCGACCGCCTTGTTTGTTCGACGGGATATCGAGGTGTGCGCCAAGGCGTTc                                                                                                                     <  1:3052163/151‑1 (MQ=14)          gATGTGTTGGCGGGGAGATCGAGCGCCGCCCGCGCGGCGCTTCGCGGGTAAACCCGCTCCTACGCTTGTTTCGGGCCAGTCCCTCCTGCGCCCGGCGCGCGCGACCGCCTTGTTTGTTCGACGGGATATCGAGGTGTGCGCCAAGGCGTTc                                                                                                                     <  1:1109354/151‑1 (MQ=14)           aTGTGTTGGCGGGGAGATCGAGCGCCGCCCGCGCGGCGCTTCGCGGGTAAACCCGCTCCTACGCTTGTTTCGGGCCAGTCCCTCCTGCGCCCGGCGCGCGCGACCGCCTTGTTTGTTCGACGGGATATCGAGGTGTGCGCCAAGGCGTTcg                                                                                                                    <  1:4843840/151‑1 (MQ=14)            tgtgTTGGCGGGGAGATCGAGCGCCGCCCGCGCGGCGCTTCGCGGGTAAACCCGCTCCTACGCTTGTTTCGGGCCAGTCCCTCCTGCGCCCGGCGCGCGCGACCGCCTTGTTTGTTCGACGGGATATCGAGGTGTGCGCCAAGGCGTTcgc                                                                                                                   <  1:400843/151‑1 (MQ=14)                  ggCGGGGAGATCGAGCGCCGCCCGCGCGGCGCTTCGCGGGTAACCCCGCTCCTACGCTTGTTTCGGGCCAGTCCCTCCTGCGCCCGGCGCGCGCGACCGCCTTGTTTGTTCGACGGGATATCGAGGTGTGCGCCAAGGCGTTCGCGCGCaa                                                                                                             <  2:1744416/151‑1 (MQ=11)                    cGGGGAGATCGAGCGCCGCCCGCGCGGCGCTTCGCGGGTAAACCCGCTCCTACGCTTGTTTCGGGCCAGTCCCTCCTGCGCCCGGCGCGCGCGACCGCCTTGTTTGTTCGACGGGATATCGAGGTGTGCGCCAAGGCGTTCGCGCGCAAAt                                                                                                           <  2:731120/151‑1 (MQ=11)                     ggggAGATCGAGCGCCGCCCGCGCGGCGCTTCGCGGGTAAACCCGCTCCTACGCTTGTTTCGGGCCAGTCCCTCCTGCGCCCGGCGCGCGCGACCGCCTTGTTTGTTCGACGGGATATCGAGGTGTGCGCCAAGGCGTTCGCGCGCAAATg                                                                                                          <  1:7060496/151‑1 (MQ=11)                      gggAGATCGAGCGCCGCCCGCGCGGCGCTTCGCGGGTAAACCCGCTCCTACGCTTGTTTCGGGCCAGTCCCTCCTGCGCCCGGCGCGCGCGACCGCCTTGTTTGTTCGACGGGATATCGAGGTGTGCGCCAAGGCGTTCGCGCGCAAATGc                                                                                                         <  2:5488545/151‑1 (MQ=11)                       ggAGATCGCGCGCCGCCCGCGCGGCGCTTTGCGGGTAAACCCGCTCCTACGCTTGTTTGGGGCCAGGCCCTCCTGTGCCCGGCGCGCGCGACCGCCTTGTTTGTTCGACGGAATATCGAGGTGTGCGCCAAGGCGTTCGCGCGCAAATGcc                                                                                                        <  2:6130069/151‑1 (MQ=11)                       ggAGATCGAGGGCCGCCCGCGCGGCGCTTCGCGGGTAAACCCACTCCTGCGCTTGTTACGGGCCAGTCCCTCCTGCGCCCGGCGCGCGCGACCGCCTTGTTTGTTCGACGGGATATCGAGGTGTGCGCCAAGGCGTTCGCGCGCAAATGcc                                                                                                        <  2:3989485/151‑1 (MQ=11)                       ggAGATCGAGCGCCGCCCGCGCGGCGCTTCGCGGGTAAACCCGCTCCTACGCTTGTTTCGGGCCAGTCCCTCCTGCGCCCGGCGCGCGCGACCGCCTTGTTTGTTCGACGGGATATCGAGGTGTGCGCCAAGGCGTTCGCGCGCAAATGcc                                                                                                        <  1:7113132/151‑1 (MQ=11)                       ggAGATCGAGCGCCGCCCGCGCGGCGCTTCGCGGGTAAACCCGCTCCTACGCTTGTTTCGGGCCAGTCCCTCCTGCGCCCGGCGCGCGCGACCGCCTTGTTTGTTCGACGGGATATCGAGGTGTGCGCCAAGGCGTTCGCGCGCAAATGcc                                                                                                        <  1:725497/151‑1 (MQ=11)                       ggAGATCGAGCGCCGCCCGCGCGGCGCTTCGCGGGTAAACCCGCTCCTACGCTTGTTTCGGGCCAGTCCCTCCTGCGCCCGGCGCGCGCGACCGCCTTGTTTGTTCGACGGGATATCGAGGTGTGCGCCAAGGCGTTCGCGCGCAAATGcc                                                                                                        <  2:6129997/151‑1 (MQ=11)                                            gggggcTTCGCGGGTAACCGCGCTCCTGCGTTTGTGTCGGGCCAGTCCCTCCTGCACCAGTCGCGCGCGACCGCCTTGTTTGTACGACGCGATATCGAGACATGCGCCAAGGCGGTCGCGCGCAAATCCCACAGGAATAATTGGCCCGaaa                                                                                   <  2:2212689/147‑1 (MQ=1)                                                  ttagcgGGGAAACCCGCTCCTTCGTTTGTTTCGGGCCAGTCCCTCCTGTGACTGGCGCGCGCGACCGCCTTGTTTGTTCAACGCGATATCGAGAAAGGCACCAAAGCGTTCGCGCGCGAATCCCACAGGCATAATTGGCCCGAAACAAACg                                                                             <  2:2402130/148‑1 (MQ=1)                                                   ccgcgattAAACCCGCTTCTACGTTTGTTTCGCGCCAGGCCCTCCTGTGCCTGACGCGCGCGACCGCCTTGTTGGTACGACGCAATAACGAGACAGGCACCAAGGCGTTCGCGCGCAAATCCCACAGGCATAATTGGCCCGAAACAAACGt                                                                            <  1:2419452/144‑1 (MQ=1)                                                      gggttAAACCCGCTCCTACGGTTGTTTCGGGCCAGTCCCTACAGTGCCTGGCGCGCGCGACCGCCTTGTTAGAGGAACGCGATATCGAGACAGGCAACAAAGCGTTCGCGCGCGAATCCCACAGGCATAATTGGCCCGAAACAAACGTAgg                                                                         <  2:157575/147‑1 (MQ=1)                                                          tacaCCCGCTCCTACGCTTGTTTCGGGCCAGTCCCTCCTGCGCCCGGCGCGCGCGACCGCCTTGTTTGTTCGACGGGATATCGAGGTGTGCGCCAAGGCGTTCGCGCGCAAATGCCACAGGCATAACTGGCCCGAAACAAACGTAGGAGca                                                                     <  1:434248/148‑2 (MQ=1)                                                          gaagcccGCGCCGACGGGTGCTTCGGGCCAGTCCCTCCTGTGCCTGGCGCGCGCGGCCGCCTTGTTGGTACGACGCGATATCGAGACAGGCACCAAGGCGTTCGCGCGCGAATCCCACAGGCATAATTGGCCCGAAACAAACGTAGGAGCg                                                                     <  2:6272506/147‑1 (MQ=1)                                                                 tcttcTACGTTTGTTTCGCGCCAGTCCCTCCTGTGCCTGGCGCGCGCGACCGCCTTGTTTGTTCGACGCGATATCGAGACAGGCACCATAGCGTTCGCGCGCGAATCCCACAGGCATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTAc                                                              <  1:100914/147‑1 (MQ=1)                                                                   gccgaCGTTTGTTGCGGGCCGGTCCCTCCTGTGCCGGGCGCGCGCGGCCGCCTTGTTTGTTCGACGCGATATCGAGACAGGCACCAAAGCGTTCGCGCGCGAATCCCACAGGCATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTAccc                                                            <  2:6605068/147‑1 (MQ=1)                                                                      tgcgcttggttCGGGCCAGTCCCTCCTGCGCCCGGCGGGCGCGCTCGTCTTGTTTGTTCGACGGGATATCGAGGTGTGCGCCAAGGCGTTCGCGCGCAAATGCCACAGGCATAACTGGCCCGAAACAAACGTAGGAGCAGGTTTACCcgcg                                                         <  1:4371480/146‑1 (MQ=1)                                                                      tacttgtgtgtCGGGCCAGTCCCTCCTGTGCCTGGCGCGCGCGAGCGCCTTGTTTGTTCGACGCGATATCGAGACAGGCACCAAAGCGTGCGCGCGCGAATCCCACAGGCATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCcgcg                                                         <  2:5963311/145‑1 (MQ=1)                                                                       acggtggtttCGAGCCGGCACCTCCTGTGCGTGGCGCGCGCGCCCGCCTTGTTGGTACGACGCGATATCGAGACAGGCACCAAGGCGTTCGCGCGCGAATCCCACAGGCATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGa                                                        <  2:6281567/145‑1 (MQ=1)                                                                        ggtgtgtttCGGGCAAGTCCTTCCTGCACCATGCGCGCGCGACCTCCTTGTTTGTACGACGCGATATCGAGACATGCGCCAAGGCGGTCGCGCGCAAATCCCACAGGAATAATTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCTCGaa                                                       <  2:5977513/147‑1 (MQ=1)                                                                        cgcttgtttCGGGCCAGTCCCTCCTGCGCCCGGCGCGCGCGGCCGCCTTGTTTGTTCGACGGGATATCGAGGTGTGCGCCAAGGCGTTCGCGCGCAAATGCCCCAGGCCTAACTGGCCCGAAACAAACGTAGGAGCAGGCTTACCCGCGaa                                                       >  2:468425/4‑151 (MQ=1)                                                                        cgcttgtttCGGGCCAGTCCCTCCTGCGCCCGGCGCGCGCGACCGCCTTGTTTGTTCGACGGGATATCGAGGTGTGCGCCAAGGCGTTCGCGCGCAAATGCCACAGGCATAACTGGCCCGAAACAAACGTAGGAGCAGGTTTACCCGCGaa                                                       >  1:6760515/4‑151 (MQ=1)                                                                        cgcttgttgCGGGCCAGGCCCTCCTGCGCCCGGCGCGCGCGACCGCCTTGTTTGTTCGACGGGATATCGAGGTGTGCGCCAAGGCGTTCGCGCGCAAATGCCACAGGCATAACTGGCCCGAAACAAACGTAGGAGCAGGTTTACCCGCGaa                                                       <  2:6268024/148‑1 (MQ=1)                                                                          ttggttgCGGGCCAGGCCATCCTGTGGCTGGCGCGCGCGACCGCCTTGTTTGTACGACGCGATATCGAGGCATGCACCAAGGCGTTCGCGCGCAAATCCCACAGGCATAATTGGCCTGAAACAAACGTAGGAGCGGGTTTACCCGCGAAgc                                                     <  1:6925476/148‑1 (MQ=1)                                                                             gtgtCGGGCGCGTCCCTCCGGCCCCAGTCGCCCGCGACCGCCTTGTTTGTACGACGCGATATCGAGACATGCGCCAAGGCGGTCGCGCGCAAATCCCACAGGAATAATGGGCCCGAAACAAACGTAGGCGCGGGTTTACCCGCGAAGcgcc                                                  <  2:403412/148‑1 (MQ=1)                                                                                                    cccggCGCGCGCGACCGCCTTGTTTGTTCGACGGGATATCGAGGTGTGCGCCAAGGCGTTCGCGCGCAAATGCCACAGGCATAACTGGCCCGCAACAAACGTAGGAGCAGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGCTTTgcg                           >  2:4579701/4‑151 (MQ=1)                                                                                                    cccggCGCGCGCGACCGCCTTGTTTGTTCGACGGGATATCGAGGTGTGCGCCAAGGCGTTCGCGCGCAAATGCCACAGGCATAACTGGCCCGAAACAAACGTAGGAGCAGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATTTgcg                           >  1:2364209/4‑151 (MQ=1)                                                                                                    cccggCGCGCGCGACCGCCTTGTTTGTTCGACGGGATATCGAGGTGTGCGCCAAGGCGTTCGCGCGCAAATGCCACAGGCATAACTGGCCCGAAACAAACGTAGGAGCAGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATGTgcg                           >  2:5594611/4‑151 (MQ=1)                                                                                                    cccggCGCGCGCGACCGCCTTGTTTGTTCGACGGGATATCGAGGTGTGCGCCAAGGCGTTCGCGCGCAAATGCCACAGGCATAACTGGCCCGAAACAAACGTAGGAGCAGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGACTTgcg                           >  2:5897315/4‑151 (MQ=1)                                                                                                                             gttcgacgGGATATCGAGGTGTGCGCCAAGGCGTTCGCGCGCAAATGCCACAGGCATAACTGGCCCGAAACAAACGTAGGAGCAGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATTTGCGCCCCAACATCAACCTCAAGGCATac  >  1:5610919/4‑151 (MQ=1)                                                                                                                                                ||                                                                                                                                   GGCGATGTTGATGTGTTGGCGGGGAGATCGAGCGCCGCCCGCGCGGCGCTTCGCGGGTAAACCCGCTCCTACGTTTGTTTCGGGCCAGTCCCTCCTGTGCCTGGCGCGCGCGACCGCCTTGTTTGTACGACGCGATATCGAGGCATGCGCCAAGGCGTTCGCGCGCAAATGCCACAGGCATAACTGGCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATTTGCGCCCCAACATCAACCTCAAGGCATAC  >  CP009974/541972‑542246

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑