Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_hsa_pgi	3,269,969	0	A	C	27.8%	41.6 / 10.5	40	intergenic (+367/+247)	yhaC/rnpB	pentapetide repeats‑related protein/RNase P, M1 RNA component
Reads supporting (aligned to +/- strand):  ref base A (7/19);  new base C (2/8);  total (9/31)
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
Rejected as consensus: Frequency below/above cutoff threshold.

GAATAAAGCGCACTCAACAATCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGCAAAAACCCGCCGAAGCGGGTTTTTACGTAAACCAGG  >  NC_000913_3_hsa_pgi/3269822‑3270105                                                                                                                                                    |                                                                                                                                         gAATAAAGCGCACTCAACAATCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATGATTCTGCCCCTCCAAAAGAAAAAAACCGCCGaa                                                                                                                                         >  2:347497/1‑149 (MQ=255) gAATAAAGCGCACTCAACAATCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGaa                                                                                                                                         <  2:132813/149‑1 (MQ=255)     aaaGCGCACTCAACAATCTGAACCCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCgg                                                                                                                                     <  1:1012737/149‑1 (MQ=255)     aaaGCGCACTCAACAATCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCgg                                                                                                                                     <  1:1159565/149‑1 (MQ=255)     aaaGCGCACTCAACAATCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCgg                                                                                                                                     <  1:352841/149‑1 (MQ=255)       aGCGCACTCAACAATCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGAAATTCATTCATCTTTCGGCCCCTCCAAAAGGAAAAACCCGCCGAAGCGGGt                                                                                                                                   >  2:1384889/1‑149 (MQ=255)         cgcACTCAACAATCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACAGTCCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGttt                                                                                                                                 <  1:949597/149‑1 (MQ=255)          gcACTCAACAATCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCTTCGGCGGGtttt                                                                                                                                <  1:423359/149‑1 (MQ=255)           cACTCAACAATCTGAAACCCGGCGGAACGGTTTATTACGTACATCAGGTAAAACTGACAGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCTTCGGCGGGttttt                                                                                                                               <  2:384545/149‑1 (MQ=18)           cACTCAACAATCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCTTCGGCGGGttttt                                                                                                                               <  1:97265/149‑1 (MQ=255)           cACTCAACAATCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCCCTTTCTTTTGGGTATAGTGTCGTGGACAGTAATTCCTCTTTCTGCCCCACCAAAAGAAAAAACCCGCCGAAGCGGGattta                                                                                                                               >  2:1377670/1‑148 (MQ=18)           cACTCAACAATCTGAAACCAGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGttttt                                                                                                                               <  1:807792/149‑1 (MQ=255)            aCTCAACAATCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCTTCGGCGGGTTTTTa                                                                                                                              <  1:66852/149‑1 (MQ=255)            aCTCAACAATCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCTTCGGCGGGTTTTTa                                                                                                                              <  2:297482/149‑1 (MQ=255)             cTCCACAATCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCGTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTAc                                                                                                                             <  1:747900/149‑1 (MQ=255)               caacaaTCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGGAAGGCATTCGAAATTGTGCCAAGTCCAAAGTAAAAAACCGCCGCTGCGGGGTGTTACgg                                                                                                                           >  1:1320854/1‑148 (MQ=17)                aacaaTCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACCGTCATTCATCTTTCTGGCCCTCCAAAAGTAAAAAACCGCCGAAGCGGGTTTTTACGTa                                                                                                                          >  1:526454/1‑149 (MQ=255)                 acaaTCTGAAACCCGCCGGAAGGGTTTATTACGTACATCAGGTAAAACTGACCGATTAGCCGCTTACTTTTGGGAATAGTGTCGTTCACAGTCATTCATCTTTCTGACCCTCCAATAGTAAAAACCCGCCGAACCGGGTTTTTACGTaa                                                                                                                         <  1:1504160/149‑1 (MQ=255)                     tCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGAGGACAGTCATTGCACATTCTGCCCAGCCAAAAGAAAAAACCCGCACAAGCAGGGTTTTACGTAAAAcc                                                                                                                     >  1:1465434/1‑148 (MQ=17)                      cTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAg                                                                                                                    <  1:1265941/149‑1 (MQ=255)                       tGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGAGTTTTTACGTAAAACAgg                                                                                                                   <  1:1485681/149‑1 (MQ=255)                        gAAACCCGCCGTAATGGTTTATTACTTACATCAGGTAAAACTGAGCGATAAGCCGCTTTCTTTTGGGTTTAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGt                                                                                                                  <  2:135554/149‑1 (MQ=17)                        gAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAACACCCGCCGAAGCGGGTTTTTACGTAAAACAGGt                                                                                                                  <  1:1277523/149‑1 (MQ=255)                        gAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGt                                                                                                                  <  1:49404/149‑1 (MQ=255)                            cccGCCGGAACGGTTTATTACGTACATCTGGTAAAACTGACCGATACGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGaaa                                                                                                              <  2:832514/149‑1 (MQ=255)                                   gAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTTGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTTACCg                                                                                                       <  1:1446275/149‑1 (MQ=255)                                     tcGGTTTTTTACGTTCATCAGGTATTACTGACCGATAAGCCGCTTTCTTTTTGGTTTAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCTCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGAt                                                                                                     <  2:223177/148‑1 (MQ=14)                                       ggTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTTTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGACGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGATaa                                                                                                   <  1:243444/149‑1 (MQ=255)                                         tttATTACGTACATCAGTTAAAACTGAACGATAAGCCGCTTTCTTTTTTGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGATAAGc                                                                                                 <  1:103645/149‑1 (MQ=255)                                                    catcatGTAAAACTTACCGATAAGCCGCTTTCATTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCACTCCAAAAGTAAAAACCCGCCGAATCGGGTTTTTACGTAAAACAGGTGAAACTGACCGATAAGCCGCTTTCtttt                                                                                      <  1:1160240/149‑1 (MQ=14)                                                          gTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGAGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGAAAAAACCCGCCGAAGCGGGTTTTTACGt                                                                                                                           >  1:72112/1‑106 (MQ=12)                                                                  gtccGAAAAGCCTCTTTCTCTTTGGCCTACTGTCTTGGACATTCATTCTTCTTTCTGACCTTCAACAAGAACAAACCCGCCGCAGCGGGTTTTTACGTAAAACAGGTTAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGt                                                                        <  2:1320854/147‑1 (MQ=11)                                                                                                              ttttttatttATGCCACTCAAAAATTACAAACCCGCCGTATCGGTTTTTTACGTAAATCATGTTAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTTTGCCCCTCCAAAAGCAAAAACccgc                            <  2:739984/142‑1 (MQ=11)                                                                                                               ttcatCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGCAGCGGGTTTTTACGTAAAACAGGTGCAACTGACCGATAAGCCGCGTTCTTTTGGGTATAGTGTCGTGGACTGTGATTCATGTTTCTGCCCCTCCAAAAGCAAAAAcccccc                           >  1:480383/1‑149 (MQ=11)                                                                                                                  ttattacTGGCCCTCCAAAATTAAAAACCCGCCGTATCGGTTTTTTACGTAAATCAGGTTAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGCAAAAACCCGCCGaa                        <  1:666704/143‑1 (MQ=11)                                                                                                                   tttttCTGGCACTCCACAATTTCAAACCCGCCGCATCGGGTTTTTACGTAAAACAGGTGAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGCAAAAACCCGCCGAAg                       <  1:1384889/147‑1 (MQ=11)                                                                                                                      ttCTGGCACTCCAAAAGGTTAAACCCGCCGTATCGGTTTTTTACGTAAATCAGTTAAAACTGACCGATAAGCCGCTTTCTTTTGTGTATATTTTCGTGGACAGTCATTAATCTTTCTGCCCCTCCAAAAGCAAAAACCCGCCGAAGCgg                    <  2:1380050/149‑1 (MQ=11)                                                                                                                           ccccTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTa                                                                                                                              >  2:1123686/1‑38 (MQ=40)                                                                                                                           ccacTCAAAAATTATAAACCCGCCGCATGGGGTTTTTACGTAAATCAGGTCAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGCAAAAACCCGCTTCGGCGGGtttt               <  2:543888/146‑1 (MQ=11)                                                                                                                            cccTCCAATTTTTAATACCCGCCGAAGAGGGATTTTACTTAAATCAGGTGAATCTCACCGATAAGCCGGTTGCTATTCGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGCAAAAACCCGCCGAAGCGGGttttt              <  1:758669/149‑1 (MQ=11)                                                                                                                                        ttaaaCCCGCCGTATCGGTTTTTTACGTAAAACAGGTTAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGCAAAAACCCGCCGAAGCGGGTTTTTACGTAAACCAgg  <  2:526454/147‑1 (MQ=255)                                                                                                                                                 ccgAAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGATAAGCCGCTTTCTTTTgg                                                                                    >  1:817260/1‑58 (MQ=35)                                                                                                                                                    |                                                                                                                                         GAATAAAGCGCACTCAACAATCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTAAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGTAAAAACCCGCCGAAGCGGGTTTTTACGTAAAACAGGTGAAACTGACCGATAAGCCGCTTTCTTTTGGGTATAGTGTCGTGGACAGTCATTCATCTTTCTGCCCCTCCAAAAGCAAAAACCCGCCGAAGCGGGTTTTTACGTAAACCAGG  >  NC_000913_3_hsa_pgi/3269822‑3270105

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑