Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP006881	1,800,870	C→A	7.6%	pseudogene (3503/16546 nt)	U712_09020 →	frameshift (+1) in homopolymer run at nucleotide position 6839 in gene

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP006881	1,800,870	0	C	A	7.6%	164.5 / 2.1	48	pseudogene (3503/16546 nt)	U712_09020	frameshift (+1) in homopolymer run at nucleotide position 6839 in gene
Reads supporting (aligned to +/- strand):  ref base C (20/24);  new base A (2/2);  total (22/26)
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

GATATCTTGCCAGTTCCCGGGTGCGAAAAATCATCATGACTTCTGGAACCACATCAAAGAAGGCAAAGAAAGCATACGATTCTTTTCTGAAGAAGAGCTTCGCGCAAATGGAGTTCCCGAAGAATTGATACAGCATCCTGACTATGTGCCTGTGCAATCTGTGATCGAAGGGAAAGACTTATTCGATCCCGGTTTCTTTCAAATCTCGCCAAAAGATGCTGAGTATATGGACCCTCAGCTTCGCCTCTTATTGCTGCACTCCTGGAAAGCGATTGA  >  CP006881/1800733‑1801008                                                                                                                                          |                                                                                                                                           gATATCTTGCCAGTTCCCGGGTGCGAAAAATCATCATGACTTCTGGAACCACATCAAAGAAGGCAAAGAAAGCATACGATTCTTTTCTGAAGAAGAGCTTCGCGCAAATGGAGTTCCCGAAGAATTGATACAGCATCCt                                                                                                                                           <  8:177413/139‑1 (MQ=255)    atCTTGCCAGTTCCCGGGTGCGAAAAATCATCATGACTTCTGGAACCACATCAAAGAAGGCAAAGAAAGCATACGATTCTTTTCTGAAGAAGAGCTTCGCGCAAATGGAGTTCCCGAAGAATTGATACAGCATCCTGAc                                                                                                                                        >  7:61015/1‑139 (MQ=255)         gCCAGTTCCCGGGTGCGAAAAATCATCATGACTTCTGGAACCACATCAAAGAAGGCAAAGAAAGCATACGATTCTTTTCTGAAGAAGAGCTTCGCGCAAATGGAGTTCCCGAAGAATTGATACAGCATCCTGACTa                                                                                                                                      <  4:299850/136‑1 (MQ=255)         gCCAGTTCCCGGGTGCGAAAAATCATCATGACTTCTGGAACCACATCAAAGAAGGCAAAGAAAGCATACGATTCTTTTCTGAAGAAGAGCTTCGCGCAAATGGAGTTCCCGAAGAATTGATACAGCATCCTGACTAtg                                                                                                                                    <  4:184296/138‑1 (MQ=255)         gCCAGTTCCCGGGTGCGAAAAATCATCATGACTTCTGGAACCACATCAAAGAACGCAAAGAAAGCATACGATTCTTTTCTGAAGAAGAGCTTCGCGCAAATGGAGTTCCCGAAGAATTGATACAGCATCCTGACTa                                                                                                                                      <  7:181806/136‑1 (MQ=255)              ttCCCGGGTGCGAAAAATCATCATGACTTCTGGAACCACATCAAAGAAGGCAAAGAAAGCATACGATTCTTTTCTGAAGAAGAGCTTCGCGCAAATGGAGTTCTCGAAGAATTGATACAGCATCCTGACTATGTGCCtg                                                                                                                              >  2:172073/1‑139 (MQ=255)                        cGAAAAATCATCATGACTTCTGGAACCACATCAAAGAAGGCAAAGAAAGCATACGATTCTTTTCTGAAGAAGAGCTTCGCGCAAATGGAGTTCCCGAAGAATTGATACAGCATCCTGACTATGTGCCTGTGCAATCtgt                                                                                                                    >  3:131955/1‑139 (MQ=255)                             aaTCATCATGACTTCTGGAACCACATCAAAGAAGGCAAAGAAAGCATACGATTCTTTTCTGAAGAAGAGCTTCGCGCAAATGGAGTTCCCGAAGAATTGATACAGCATCCTGACTATGTGCCTGTGCAATCTGTGATCg                                                                                                               <  1:250205/139‑1 (MQ=255)                                   catGACTTCTGGAACCACATCAAAGAAGGCAAAGAAAGCATACGATTCTTTTCTGAAGAAGAGCGTCGCGCAAATTGAGTTCCCGAAGAATAGATACAGCATCCTGACTATGTGCCTGTGCAATCTGTGATCGAAGGGa                                                                                                         <  3:20158/139‑1 (MQ=255)                                    atGACTTCTGGAACCACATCAAAGAAGGCAAAGAAAGCATACGATTCTTTTCTGAAGAAGAGCTTCGCGCAAATGGAGTTCCCGAAGAATTGATACAGCATCCTGACTATGTGCCTGTGCAATCTGTGATCGAAGGGa                                                                                                         <  4:69637/138‑1 (MQ=255)                                    atGACTTCTGGAACCACATCAAAGAAGGCAAAGAAAGCATACGATTCTTTTCTGAAGAAGAGCTTCGCGCAAATGGAGTTCCCGAAGAATTGATACAGCATCCTGACTATGTGCCTGTGCAATCTGTGATCGAAGGGa                                                                                                         <  8:297843/138‑1 (MQ=255)                                           cTGGAACCACATCAAAGAAGGCAAAGAAAGCATACGATTCTTTTCTGAAGAAGAGCTTCGCGCAAATGGAGTTCCCGAAGAATTGATACAGCATCCTGACTATGTGCCTGTGCAATCTGTGATCGAAGGGa                                                                                                         >  5:199856/1‑131 (MQ=255)                                           cTGGAACCACATCAAAGAAGGCAAAGAAAGCATACGATTCTTTTCTGAAGAAGAGCTTCGCGCAAATGGAGTTCCCGAAGAATTGATACAGCATCCTGACTATGTGCCTGTGCAATCTGTGATCGAAGGGa                                                                                                         <  6:199856/131‑1 (MQ=255)                                              gAACCACATCAAAGAAGGCAAAGAAAGCATACGATTCTTTTCTGAAGAAGAGCTTCGCGCAAATGGAGTTCCCGAAGAATTGATACAGCATCCTGACTATGTGCCTGTGCAATCTGTGATCGAAGGGAAAGACTTAtt                                                                                               <  8:63412/138‑1 (MQ=255)                                                 ccACATCAAAGAAGGCAAAGAAAGCATACGATTCTTTTCTGAAGAAGAGCTTCGCGCAAATGGAGTTCCCGAAGAATTGATACAGCATCCTGACTATGTGCCTGTGCAATCTGTGATCGAAGGGAAAGACTTATTCGAt                                                                                           >  3:103203/1‑139 (MQ=255)                                                              ggCAAAGAAAGCATACGATTCTTTTCTGAAGAAGAGCTTCGCGCAAATGGAGTTCCCGAAGAATTGATACAGCATCCTGACTATGTGCCTGTGCAATCTGTGATCGAAGGGAAAGACTTATTCGATCCCGGtttcttt                                                                               >  2:81512/1‑138 (MQ=255)                                                                  aagaaagCATACGATTCTTTTCTGAAGAAGAGCTTCGCGCGAATGGAGTTCCCGAAGAATTGATACAGCATCCTGACTATGTGCCTGTGCAATCTGTGATCGAAGGGAAAGACTTATTCGATCCCGGTTTCTTTCAAAt                                                                          <  3:94584/139‑1 (MQ=255)                                                                      aagCATACGATTCTTTTCTGAAGAAGAGCTTCGCGCAAATGGAGTTCCCGAAGAATTGATACAGCATCCTGACTATGTGCCTGTGCAATCTGTGATCGAAGGGAAAGACTTAtt                                                                                               <  1:131869/114‑1 (MQ=255)                                                                      aagCATACGATTCTTTTCTGAAGAAGAGCTTCGCGCAAATGGAGTTCCCGAAGAATTGATACAGCATCCTGACTATGTGCCTGTGCAATCTGTGATCGAAGGGAAAGACTTAtt                                                                                               >  2:131869/1‑114 (MQ=255)                                                                      aagCATACGATTCTTTTCTGAAGAAGAGCTTCGCGCAAATGGAGTTCCCGAAGAATTGATACAGCATCCTGACTATGTGCCTGTGCAATCTGTGATCGAAGGGAAAGACTTATTCGATCCCGGTTTCTTTCAAATCTCg                                                                      >  3:256217/1‑139 (MQ=255)                                                                       agCATACGATTCTTTTCTGAAGAAGAGCTTCGCGCAAATGGAGTTCCCGAAGAATTGATACAGCATCCTGACTATGTGCCTGTGCAATCTGTGATCGAAGGGAAAGACTTATTCGATCCCGGTTTCTTTCAAATCTCGc                                                                     >  1:176472/1‑139 (MQ=255)                                                                         cATTCGATTCTTTTCTGAAGAATAGCTTCGCGCAAATGGAGTTCCCGAAGAATTGATACAGCATCATGACTATGTGCCTGTGCAAt                                                                                                                        >  7:173895/1‑86 (MQ=255)                                                                         cATACGATTCTTTTCTGAAGAAGAGCTTCGCGCAAATGGAGTTCCCGAAGAATTGATACAGCATCCTGACTATGTGCCTGTGCAATCTGTGATCGAAGGGAAAGACTTATTCGATCCCGGTTTCTTTCAAATCTCGcc                                                                    >  2:33249/1‑138 (MQ=255)                                                                         cATACGATTCTTTTCTGAAGAAGAGCTTCGCGCAAATGGAGTTCCCGAAGAATTGATACAGCATCCTGACTATGTGCCTGTGCAATCTGTGATCGAAGGGAAAGACTTATTCGATCCCGGTTTCTTTCAAATCTCGcc                                                                    >  4:227179/1‑138 (MQ=255)                                                                         cATACGATTCTTTTCTGAAGAAGAGCTTCGCGCAAATGGAGTTCCCGAAGAATTGATACAGCATCATGACTATGTGCCTGTGCAAt                                                                                                                        <  8:173895/86‑1 (MQ=255)                                                                         cATACGATTCTTTTCTGAAGAAGAGCTTCGCGCAAATGGAGTTCCCGAAGAATTGATACAGCATCATGACTATGTGCCTGTGCAAt                                                                                                                        >  5:82000/1‑86 (MQ=255)                                                                         cATACGATTCTTTTCTGAAGAAGAGCTTCGCGCAAATGGAGTTCCCGAAGAATTGATACAGCATCATGACTATGTGCCTGTGCAAt                                                                                                                        <  6:82000/86‑1 (MQ=255)                                                                               aTTCTTTTCTGAAGAAGAGCTTCGCGCAAATGGAGTTCCCGAAGAATTGATACAGCATCCTGACTATGTGCCTGTGCAATCTGTGATCGAAGGGAAAGACTTATTCGATCCCGGTTTCTTTCAAATCTCGCCAAAAGAt                                                             >  5:13131/1‑139 (MQ=255)                                                                                   ttttCTGAAGAAGAGCTTCGCGCAAATGGAGTTCCCGAAGAATTGATACAGCATCCTGACTATGTGCCTGTGCAATCTGTGATCGAAGGGAAAGACTTATTCGATCCCGGTTTCTTTCAAATCTCGCCAAAAGATGCt                                                          >  1:57085/1‑138 (MQ=255)                                                                                     ttCTGAAGAAGAGCTTCGCGCAAATGGAGTTCCCGAAGAATTGATACAGCATCCTGACTATGTGCCTGTGCAATCTGTGATCGAAGGGAAAGACTTATTCGATCCCGGTTTCTTTCAAATCTCGCCAAAAGATGCt                                                          <  6:13131/136‑1 (MQ=255)                                                                                     ttCTGAAGAAGAGCTTCGCGCAAATGGAGTTCCCGAAGAATTGATACAGCATCCTGACTATGTGCCTGTGCAATCTGTGATCGAAGGGAAAGACTTATTCGATCCCGGTTTCTTTCAAATCTCGCCAAAAGATGCt                                                          <  1:270972/136‑1 (MQ=255)                                                                                     ttCTGAAGAAGAGCTTCGCGCAAATGGAGTTCCCGAAGAATTGATACAGCATCCTGACTATGTGCCTGTGCAATCTGTGATCGAAGGGAAAGACTTATTCGATCCCGGTTTCTTTCAAATCTCGCCAAAAGATGCt                                                          <  4:60475/136‑1 (MQ=255)                                                                                     ttCTGAAGAAGAGCTTCGCGCAAATGGAGTTCCCGAAGAATTGATACAGCATCCTGACTATGTGCCTGTGCAATCTGTGATCGAAGGGAAAGACTTATTCGATCCCGGTTTCTTTCAAATCTCGCCAAAAGATGCt                                                          <  4:131955/136‑1 (MQ=255)                                                                                     ttCTGAAGAAGAGCTTCGCGCAAATGGAGTTCCCGAAGAATTGATACAGCATCCTGACTATGTGCCTGTGCAATCTGTGATCGAAGGGAAAGACTTATTCGATCCCGGTTTCTTTCAAATCTCGCCAAAAGATGCt                                                          <  8:61015/136‑1 (MQ=255)                                                                                     ttCTGAAGAAGAGCTTCGCGCAAATGGAGTTCCCGAAGAATTGATACAGCATCCTGACTATGTGCCTGTGCAATCTGTGATCGAAGGGAAAGACTTATTCGATCCCGGTTTCTTTCAAATCTCGCCAAAAGATGCTg                                                         <  1:304187/137‑1 (MQ=255)                                                                                     ttCTGAAGAAGAGCTTCGCGCAAATGGAGTTCCCGAAGAATTGATACAGCATCCTGACTATGTGCCTGTGCAATCTGTGATCGAAGGGAAAGACTTATTCGATCCCGGTTTCTTTAAAATCTCGCCAAAAGATGCTg                                                         <  2:176472/137‑1 (MQ=255)                                                                                        tGAAGAAGAGCTTCGCGCAAATGGAGTTCCCGAAGAATTGATACAGCATCCTGACTATGTGCCTGTGCAATCTGTGATCGAAGGGAAAGACTTCTTCGATCCCGGTTTCTTTCAAATCTCGCCAAAAGATGCTGAGta                                                     >  2:149530/1‑138 (MQ=255)                                                                                          aagaagAGCTTCGCGCAAATGGAGTTCCCGAAGAATTGATACAGCATCCTGACTATGTGCCTGTGCAATCTGTGATCGAAGGGAAAGACTTATTCGATCCCGGTTTCTTTCAAATCTCGCCAAAAGATGCTGAGTatat                                                  <  4:219495/139‑1 (MQ=255)                                                                                                                  ttCCCGAAGAATTGATACAGCATCCTGACTATGTGCCTGTGCAATCTGTGATCGAAGGGAAAGACTTATTCGATCCCGGTTTCTTTCAAATCTCGCCAAAAGATGCt                                                          <  4:241374/107‑1 (MQ=255)                                                                                                                  ttCCCGAAGAATTGATACAGCATCCTGACTATGTGCCTGTGCAATCTGTGATCGAAGGGAAAGACTTATTCGATCCCGGTTTCTTTCAAATCTCGCCAAAAGATGCt                                                          >  3:241374/1‑107 (MQ=255)                                                                                                                    cccGAAGAATTGATACAGCATCCTGACTATGTGCCTGTGCAATCTGTGATCGAAGGGAAAGACTTATTCGATCCCGGTTTCTTTCAAATCTCGCCAAAAGATGCt                                                          >  5:217414/1‑105 (MQ=255)                                                                                                                    cccGAAGAATTGATACAGCATCCTGACTATGTGCCTGTGCAATCTGTGATCGAAGGGAAAGACTTATTCGATCCCGGTTTCTTTCAAATCTCGCCAAAAGATGCt                                                          <  6:217414/105‑1 (MQ=255)                                                                                                                    cccGAAGAATTGATACAGCATCCTGACTATGTGCCTGTGCAATCTGTGATCGAAGGGAAAGACTTATTCGATCCCGGTTTCTTTCAAATCTCGCCAAAAGATGCTGAGTATATGGACCCTCAGCTTCGCCTCTTATtgc                        >  7:179785/1‑139 (MQ=255)                                                                                                                        aagaaTTGATACAGCATCCTGACTATGTGCCTGTGCAATCTGTGATCGAAGGGAAAGACTTATTCGATCCCGGTTTCTTTCAAATCTCGCCAAAAGATGCTGAGTATATGGACCCTCAGCTTCGCCTCTTATTGCTGCa                    <  3:227179/139‑1 (MQ=255)                                                                                                                             ttGATACAGCATCCTGACTATGTGCCTGTGCAATCTGTGATCGAAGGGAAAGACTTATTCGATCCCGGTTTCTTTCAAAt                                                                          >  4:313616/1‑80 (MQ=255)                                                                                                                             ttGATACAGCATCCTGACTATGTGCCTGTGCAATCTGTGATCGAAGGGAAAGACTTATTCGATCCCGGTTTCTTTCAAAt                                                                          <  3:313616/80‑1 (MQ=255)                                                                                                                                     gCATCCTGACTATGTGCCTGTGCAATCTGTGATCGAAGGGAAAGACTTATTCGATCCCGGTTTCTTTCAAATCTCGCCAAAAGATGCTGAGTATATGGACCCTCAGCTTCGCCTCTTATTGCTGCACTCCTGGAAAGc        >  3:99526/1‑138 (MQ=255)                                                                                                                                     gCATCCTGACTATGTGCCTGTGCAATCTGTGATCGAAGGGAAAGACTTATTCGATCCCGGTTTCTTTCAAATCTCGCCAAAAGATGCTGAGTATATGGACCCTCAGCTTCGCCTCTTATTGCTGCACTCCTGGAAAGc        >  2:96254/1‑138 (MQ=255)                                                                                                                                          cTGACTATGTGCCTGTGCAATCTGTGATCGAAGGGAAAGACTTATTCGATCCCGGTTTCTTTCAAATCTCGCCAAAAGATGCTGAGTATATGGACCCTCAGCTTCGCCTCTTATTGCTGCACTCCTGGAAAGCGATTGa  <  1:172073/139‑1 (MQ=255)                                                                                                                                          cTGACTATGTGCCTGTGCAATCTGTGATCGAAGGGAAAGACTTATTCGATCCCGGTTTCTTTCAAATCTCGCCAAAAGATGCTGAGTATATGGACCCTCAGCTTCGCC‑CTTATTGCTGCACTCCTGGAAAGCGATTg   >  5:145408/1‑137 (MQ=255)                                                                                                                                          |                                                                                                                                           GATATCTTGCCAGTTCCCGGGTGCGAAAAATCATCATGACTTCTGGAACCACATCAAAGAAGGCAAAGAAAGCATACGATTCTTTTCTGAAGAAGAGCTTCGCGCAAATGGAGTTCCCGAAGAATTGATACAGCATCCTGACTATGTGCCTGTGCAATCTGTGATCGAAGGGAAAGACTTATTCGATCCCGGTTTCTTTCAAATCTCGCCAAAAGATGCTGAGTATATGGACCCTCAGCTTCGCCTCTTATTGCTGCACTCCTGGAAAGCGATTGA  >  CP006881/1800733‑1801008

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑