Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	3,377,782	A→G	9.7%	intergenic (‑155/‑280)	mdh ← / → argR	malate dehydrogenase, NAD(P)‑binding/l‑arginine‑responsive arginine metabolism regulon transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	3,377,782	0	A	G	9.7%	117.6 / 3.4	41	intergenic (‑155/‑280)	mdh/argR	malate dehydrogenase, NAD(P)‑binding/l‑arginine‑responsive arginine metabolism regulon transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base A (18/19);  new base G (2/2);  total (20/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.79e-01

AGTTCTGAACCTGAAGGCAGTTGGGTTTTTAACAGTAGTGCAAGCGCCTGGCCAATACCGCCAGCAGCGCCGAGGACTGCGACTTTCATCCTAAACTCCTTATTATATTGATAAACTAAGATATGTTGCTCCGCTGCCGCGACCTTAATCCACAAAATTGCCGTTTACAATGACCACATCTCAAGAATGTGTAGTCACGCAAGTTTAGCGTTTATGCATTTAATTGCCGTAATCAGGAACCTAACTTACGTAATTAACAGTCGCTTATGCATTAGCGCAACATTCCAACAGGTGGTGACAATATACCCTACCGTTCAGCCAAAACAACATCAATTTGATAACAATTAATTTACTTTTAAGCAGAATTTGCATGCCGTGACGCAGGCATGTTTCTCAATAACGAAATTTGATAAAATCCCGCTCTTTCATAACATTATTTCAGCCTTCTTCAGGGCTGACTGTTTGCATAAAAATTCA  >  CP009273/3377539‑3378015                                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                          agTTCTGAACCTGAAGGCAGTTGGGTTTTTAACAGTAGTGCAAGCGCCTGGCCAATACCGCCAGCAGCGCCGAGGACTGCGACTTTCATCCTAAACTCCTTATTATATTGATAAACTAAGATATGTTGCTCCGCTGCCGCGACCTTAATCCACAAAATTGCCGTTTACAATGACCACATCCCAAGAATGTGTCGTCACGCAAGTTTAGCGTTTATGCATTTAATAGCCGTAAGCAGGAACCTAAATTCAATACTTAACATTCTCtttttttttt                                                                                                                                                                                                             >  2:361345/1‑266 (MQ=255)                  cAGTTGGGTTTTTAACAGTAGTGCAAGCGCCTGGCCAATACCGCCAGCAGCGCCGAGGACTGCGACTTTCATCCTAAACTCCTTATTAGAGTGATAAACTAAGATATGTTGCTCCGCTGCCGCGACCTTAATCCACAAAATTGCCGTTTACAATGACCACATCTCAAGAATGTGTAGTCACGCAAGTTTAGCGTTTATGCATTTAATTGCCGTAATCAGGAACCTAACTTACGTAATTAACAGTCGCTTATGCATTAGCGCAACATTCCAACAg                                                                                                                                                                                            <  1:449766/274‑1 (MQ=255)                                                                         aGGACTGCGACTTTCATCCTAAACTCCTTATTATATTGATAAACTAAGATATGTTGCTCCGCTGCCGCGACCTTAATCCACAAAATTGCCGTTTACAATGACCACATCTCAAGAATGTGTAGTCACGCAAGTTTAGCGTTTATGCATTTAATTGCCGTAATCAGGAACCTAACTTACGTAATTAACAGTCGCTTATGCATTAGCGCAACATTCCAACAGGTGGTGACAATATACCCTACCGTTCAGCCAAAAAAACATAAATTTGAAAAAaataa                                                                                                                                    >  1:5716/1‑273 (MQ=255)                                                                                                   cTTATTATATTGATAAACTAAGATATGTTGCTCCGCTGCCGCGACCTTAATCCACAAAATTGCCGTTTACAATGACCACATCTCAAGAATGTGTAGTCACGCAAGTTTAGCGTTTATGCATTTAATTGCCGTAATCAGGAACCTAACTTACGTAATTAACAGTCg                                                                                                                                                                                                                        >  1:182200/1‑165 (MQ=255)                                                                                                   cTTATTATATGGATAAACTAAGATATGTTGCTCCGCTGCCGCGACCTTAATCCACAAAATTGCCGTTTACAATGACCACATCTCAAGAATGTGTAGTCACGCAAGTTTAGCGTTTATGCATTTAATTGCCGTAATCAGGAACCTAACTTACGTAATTAACAGTCGCTTATGCATTAGCGCAACATTCCAACAgg                                                                                                                                                                                           >  1:741938/1‑194 (MQ=255)                                                                                                       ttatATTGATAAACTAAGATATGTTGCTCCGCTGCCGCGACCTTAATCCACAAAATTGCCGTTTACAATGACCACATCTCAAGAATGTGTAGTCACGCAAGTTTAGCGTTTATGCATTTAATTGCCGTAATCAGGAACCTAACTTACGTAATTAACAGTCGCTTa                                                                                                                                                                                                                    <  2:182198/165‑1 (MQ=255)                                                                                                             tGATAAACTAAGATATGTTGCTCCGCTGCCGCGACCTTAATCCACAAAATTGCCGTTTACAATGACCACATCTCAAGAATGTGTAGTCACGCAAGTTTAGCGTTTATGCATTTAATTGCCGTAATCAGGAACCTAACTTACGTAATTAACAGTCGCTTATGCATTAGCGCAACAtt                                                                                                                                                                                                   >  2:51100/1‑176 (MQ=255)                                                                                                               aTAAACTAAGATATGTTGCTCCGCTGCCGCGACCTTAATCCACAAAATTGCCGTTTACAATGACCACATCTCAAGAATGTGTAGTCACGCAAGTTTAGCGTTTATGCATTTAATTGCCGTAATCAGGAACCTAACTTACGTAATTAACAGTCGCTTATGCATTATCGCAACATTCCAACAGGTTGTGACAATATACCCTACCGTTCAGCCAAAACAACATCAATTTTAAAACAATTAATTTACTTTTAAACAAAATTTACAATCCGttcaaccaa                                                                                              >  2:504773/1‑267 (MQ=255)                                                                                                                 aaaCTAAGATATGTTGCTCCGCTGCCGCGACCTTAATCCACAAAATTGCCGTTTACAATGACCACATCTCAAGAATGTGTAGTCACGCAAGTTTAGCGTTTATGCATTTAATTGCCGTAATCAGGAACCTAACTTACGTAATTAACAGTCGCTTATGCATTAGCGCAACATTCCaa                                                                                                                                                                                               <  1:51101/176‑1 (MQ=255)                                                                                                                              ttGCTCCGCTGCCGCGACCTTAATCCACAAAATTGCCGTTTACAATGACCACATCTCAAGAATGTGTAGTCACGCAAGTTTAGCGTTTATGCATTTAATTGCCGTAATCAGGAACCTAACTTACg                                                                                                                                                                                                                                     >  2:154620/1‑125 (MQ=255)                                                                                                                                  tCCGCTGCCGCGACCTTAATCCACAAAATTGCCTTTTACAATGACCACATCTCAAGAATGTGTAGTCACGCAAGTTTAGCGTTTATGCATTTAATTGCCGTAATCAGGAACCTAACTTACGTAAt                                                                                                                                                                                                                                 <  1:154621/125‑1 (MQ=255)                                                                                                                                      cttaatcaaattaaaTCCACAAAATTTCCTGTTACAATGCCAACATCTCATGAATGTGTAGTCTCGCTAGTTTTGCGTTTATTCATTTAATTGCCCTAATCAGGAACCTAACTTACGTAATTAACAGTCTCTTATGCATTAGCGCAACATTCCAACAGGTCGTGACAATATACCCTACCGTTCATCCAAAACAACATCAATTTGATAACAACTAATTTACTTTTAAGCAGAATTTGCATGCCGTGACGCAGGCATGTTTCTCAATAACGAAAtt                                                                        <  2:5716/261‑1 (MQ=255)                                                                                                                                           gcgACCTTAATCCACAAAATTGCCGTTTACAATGACCACATCTCAAGAATGTGTAGTCACGCAAGTTTAGCGTTTATGCATTTAATTGCCGTAATCAGGAACCTAACTTACGTAAtt                                                                                                                                                                                                                                >  1:8439/1‑117 (MQ=255)                                                                                                                                               ccTTAATCCACAAAATTGCCGTTTACAATGACCACATCTCAAGAATGTGTAGTCACGCAAGTTTAGCGTTTATGCATTTAATTGCCGTAATCAGGAACCTAACTTACGTAATTAACa                                                                                                                                                                                                                            <  2:8439/117‑1 (MQ=255)                                                                                                                                                   aaTCCACAAAATTGCCGTTTACAATGACCACATCTCAAGAATGTGTAGTCACGCAAGTTTAGCGTTTATGCATTTAATTGCCGTAATCAGGAACCTAACTTACGTAATTAACAGTCGCTTATGCATTAGCGCAACATTCCAACAGGTGGTGACAATATACCCTACCGTTCAGCCAAAACAACATCAATTTGATAACAATTAATTTACTTTTAAGCAGAATTTGCATGCCGTGACGCAGGCATGTTTCTCAATAACGAAATTTGATAAAATCCCGc                                                          >  1:200344/1‑275 (MQ=255)                                                                                                                                                         caAAATTGCCGTTTACAATGACCACATCTCAAGAATGTGTAGTCACGCAAGTTTAGCGTTTATGCATTTAATTGCCGTAATCAGGAACCTAACTTACGTAATTAACAGTCGCTTATGCATTAGCGCAACATTCCAACAGGTGGTGAc                                                                                                                                                                                    >  2:12317/1‑147 (MQ=255)                                                                                                                                                            aaTTGCCGTTTACAATGACCACATCTCAAGAATGTGTAGTCACGCAAGTTTAGCGTTTATGCATTTAATTGCCGTAATCAGGAACCTAACTTACGTAATTAACAGTCGCTTATGCATTAGCGCAACATTcacac                                                                                                                                                                                              >  2:387245/1‑130 (MQ=255)                                                                                                                                                             aTTGCCGTTTACAATGACCACATCTCAAGAATGTGTAGTCACGCAAGTTTAGCGTTTATGCATTTAATTGCCGTAATCAGGAACCTAACTTACGTAATTAACAGTCGCTTATGCATTAGCGCAACATTCCAACAGGTGGTGACAata                                                                                                                                                                                <  1:12317/147‑1 (MQ=255)                                                                                                                                                                gCCGTTTACAATGACCACATCTCAAGAATGTGTAGTCACGCAAGTTTAGCGTTTATGCATTTAATTGCCGTAATCAGGAACCTAACTTACGTAATTAACAGTCGCTTATGCATTAGCGCAACATTCCAACAggt                                                                                                                                                                                          <  1:387252/134‑1 (MQ=255)                                                                                                                                                                                              tgtAGTCACGCAAGTTTAGCGTTTATGCATTTAATTGCCGTACTCAGGAACCTAGCTTACGTAATTAACAGTCGCTTATGCATTAGCGCAACATTCCAACAGGTGGTGACAATATACCCTACAGTTCAGCCAAAACAACATCAATTTGATAACAATTAATTCACTTTTACGCAGAATTTGCATGCCGTGACGCAGGCATGTTTCTCAATAACGAAATTTAATAAAATACACCTCTTTATTAAACTTATAGCAGACttcttcctttttcttttcc                >  2:365285/1‑261 (MQ=255)                                                                                                                                                                                              tgtAGTCACGCAAGTTTAGCGTTTATGCATTTAATTGCCGTAATCAGGAACCTAGCTTACGTAATTAACAGTCGCTTATGCATTAGCGCAACATTCAAACAGGTGGTGACAATATACCCTACCGTTCAGcc                                                                                                                                                               >  1:427540/1‑131 (MQ=255)                                                                                                                                                                                              tgtAGTCACGCAAGTTTAGCGTTTATGCATTTAATTGCCGTAATCAGGAACCTAACTTACGTAAtt                                                                                                                                                                                                                                >  1:270308/1‑66 (MQ=255)                                                                                                                                                                                              tgtAGTCACGCAAGTTTAGCGTTTATGCATTTAATTGCCGTAATCAGGAACCTAACTTACGTAATTAACAGTCGCTTATGCATTAGCGCAACATTCCAACAGGTGGTGa                                                                                                                                                                                     >  2:180468/1‑109 (MQ=255)                                                                                                                                                                                                tAGTTACTCAAGTTTAGCGTTTATGCATTTAATTGCCGTAATCAGGAACCTAACTTACGTAATTAACAGTCGCTTATGCATTATCGCAACATTCCAACAGGTGGTGACAATATACCCTACCGTTCAGCCAAAACAACATCAATTTGATAACAATTAATTTACTTTTAAGCAGAATTTGCATGCCGTGACGCAGGCATGTTTCTCAATAACGAAATTTGATAAAATCCCGCTCTTTCATAACATTAttt                                        <  1:49558/248‑1 (MQ=255)                                                                                                                                                                                                  gTCACGCAAGTTTAGCGTTTATGCATTTAATTGCCGTAATCAGGAACCTAGGTTACGTAATTAACAGTCGCTTAGGCATTAGCGCAACATTCCAACAGGTGGTGACAATATACCCTACCGTTCAGCCAAAACAACATCAATTTGATAACAATTAATTTACTTTTAAGCAGAATTTGCATGCCGTGACGCAGGCATGTTTCTCAATAACGAAATTTGATAAAATCCCGCTCTTTCATAACATTAttt                                        <  1:365292/246‑1 (MQ=255)                                                                                                                                                                                                  gTCACGCAAGTTTAGCGTTTATGCATTTAATTGCCGTAATCAGGAACCTAGCTTACGTAATTAACAGTCGCTTATGCATTAGCGCAACATTCAAACAGGTGGTGACAATATACCCTACCGTTCAGCCaaaa                                                                                                                                                           <  2:427533/131‑1 (MQ=255)                                                                                                                                                                                                  gTCACGCAAGTTTAGCGTTTATGCATTTAATTGCCGTAATCAGGAACCTAAc                                                                                                                                                                                                                                          <  1:350754/52‑1 (MQ=255)                                                                                                                                                                                                  gTCACGCAAGTTTAGCGTTTATGCATTTAATTGCCGTAATCAGGAACCTAACTTACGTAATTAACa                                                                                                                                                                                                                            <  2:270304/66‑1 (MQ=255)                                                                                                                                                                                                  gTCACGCAAGTTTAGCGTTTATGCATTTAATTGCCGTAATCAGGAACCTAACTTACGTAATTAACAGTCGCTTATGCATTAGCGCAACATTCCAACAGGTGGTGACAat                                                                                                                                                                                 <  1:180470/109‑1 (MQ=255)                                                                                                                                                                                                         aaGTTTAGCGTTTATGCATTTAATTGCCGTAATCATGAACCTAACTTACGTAATTAACAGTCGCTTATGCATTAGCGCAACATTCCAACAGGTGGTGACAATATACCCTACCGTTCAGCCAAAACAACATCAATTTGATAACAATTAATTTACTTTTAAGCAGAATTTGCATGCCGTGACGCAGGCATGTTTCTCAATAACGAAATTTGATAAAATCCCGCTCTTTCATAACATTATTTCAGCCTTCTTCAGGGCTGACTGTTTGCATAAAAAtt    <  1:361352/275‑1 (MQ=255)                                                                                                                                                                                                           gTTTAGCGTTTATGCATTTAATTGCCGTAATCAGGAACCTAACTTACGTAATTAACAGTCGCTTATGCATTAGCGCAACATTCCAACAGGTNGTGACAATATACCCTACCGTTCAGCCAAAACAACATCAATTTGATAACAATTAATTTACTTTTAAGCAGAATTTGCATGCCGTGACGCAGGCATGTTTCTCAATAACGAAATTTGATAAAATCCCGCTCTTTCATAACATTATTTCAGCCTTCTCCAGCGCTGACTGTTTGCATAAAAATTCa  <  1:504782/275‑1 (MQ=255)                                                                                                                                                                                                                 cGTTTATGCATTTAATTGCCGTAATCAGGAACCTAACTTACGTAATTAACAGTCGCTTATGCATTAGCGCAACATTCCAACAgg                                                                                                                                                                                           >  1:162296/1‑84 (MQ=255)                                                                                                                                                                                                                     tATGCATTTAATTGCCGTAATCAGGAACCTAACTTACGTaa                                                                                                                                                                                                                                  >  2:648317/1‑41 (MQ=255)                                                                                                                                                                                                                     tATGCATTTAATTGCCGTAATCAGGAACCTAACTTACGTAATTAACAGTCGCTTATGCATTAGCGCAACATTCCAACAggtggt                                                                                                                                                                                       <  2:162294/84‑1 (MQ=255)                                                                                                                                                                                                                     tATGCATTTAATTGCCGTAATCAGGAACCTAACTTACGTAATTAACAGTCGCTTATGCATTAGCGCAACATTCCAACAggtggt                                                                                                                                                                                       >  2:151108/1‑84 (MQ=255)                                                                                                                                                                                                                     tATGCATTTAATTGCCGTAATCAGGAACCTAACTTACGTAATTAACAGTCGCTTATGCATTAGCGCAACATTCCAACAGGTGGTGACAATATACCCTACCGTTAAGCCAAAACAACATCAATTTGATAACAATTAATTTACTTTTAAGCAGAATTTGCATGCCGTGACGCAGGCATGTTTCTCAATAACGAAATTTGATAAAATc                                                              >  2:234083/1‑205 (MQ=255)                                                                                                                                                                                                                         cATTTAATTGCCGTAATCAGGAACCTAACTTACGTAATTaa                                                                                                                                                                                                                              <  1:648331/41‑1 (MQ=255)                                                                                                                                                                                                                         cATTTAATTGCCGTAATCAGGAACCTAACTTACGTAATTAACAGTCGCTTATGCATTAGCGCAACATTCCAACAGGTGGTGACa                                                                                                                                                                                   <  1:151109/84‑1 (MQ=255)                                                                                                                                                                                                                         cATTTAATTGCCGTAATCAGGAACCTAACTTACGTAATTAACAGTCGCTTATGCATTAGCGCAACATTCCAACAGGTGGTGACAATATACCCTACCGTTCAGCCAAAACAACATCAATTTGATAACAATTAATTTACTTTTAAGCAGAATTTGCATGCCGTGACGCAGGCATGTTTCTCAATAACGAAATTTGATAAAATCCCGc                                                          <  1:234085/205‑1 (MQ=255)                                                                                                                                                                                                                           tttAATTGCCGTAATCAGGAACCTAACTTACGTAATTaa                                                                                                                                                                                                                              >  2:294067/1‑39 (MQ=255)                                                                                                                                                                                                                               aTTGCCGTAATCAGGAACCTAACTTACGTAATTAACAGt                                                                                                                                                                                                                          <  1:294072/39‑1 (MQ=255)                                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                          AGTTCTGAACCTGAAGGCAGTTGGGTTTTTAACAGTAGTGCAAGCGCCTGGCCAATACCGCCAGCAGCGCCGAGGACTGCGACTTTCATCCTAAACTCCTTATTATATTGATAAACTAAGATATGTTGCTCCGCTGCCGCGACCTTAATCCACAAAATTGCCGTTTACAATGACCACATCTCAAGAATGTGTAGTCACGCAAGTTTAGCGTTTATGCATTTAATTGCCGTAATCAGGAACCTAACTTACGTAATTAACAGTCGCTTATGCATTAGCGCAACATTCCAACAGGTGGTGACAATATACCCTACCGTTCAGCCAAAACAACATCAATTTGATAACAATTAATTTACTTTTAAGCAGAATTTGCATGCCGTGACGCAGGCATGTTTCTCAATAACGAAATTTGATAAAATCCCGCTCTTTCATAACATTATTTCAGCCTTCTTCAGGGCTGACTGTTTGCATAAAAATTCA  >  CP009273/3377539‑3378015

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑