Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913_3_hsa_pgi	1,466,201	T→C	21.4%	pseudogene (810/2513 nt)	ydbA →	pseudogene, autotransporter homolog; interrupted by IS2 and IS30

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_hsa_pgi	1,466,201	0	T	C	21.4%	46.5 / 9.5	32	pseudogene (810/2513 nt)	ydbA	pseudogene, autotransporter homolog; interrupted by IS2 and IS30
Reads supporting (aligned to +/- strand):  ref base T (3/22);  new base C (4/3);  total (7/25)
Fisher's exact test for biased strand distribution p-value = 2.58e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.25e-01

GTGATAATGCCACAGTAAACAACAATGGCAAAACCACCGTTGACGGTAAAGATTCCACCGGTACGGAAATCAACGGTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGC‑GGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCATCGTCAATAACGAAGGCGAGAGCACCATCACCAACGGTGGCACCGGCACCCAGATTAATGGT  >  NC_000913_3_hsa_pgi/1466053‑1466348                                                                                                                                                      |                                                                                                                                                    gTGATAATGCCACAGTAAACAACAATGGCAAAACCACCGTTGACGGTAAAGATTCCACCGGTACGGAAATCAACGGTAATAACGGGAAAGTTATTCAGGACGGCGATCTGGATGTCAGCGGCGGC‑GGTCACGGTATTGATATCACCGGt                                                                                                                                                     >  1:284653/1‑149 (MQ=255)      aaTGCCACAGTAAACACCAATGGCAAAACCACCGTTGACGGTAAAGATTCCACCGGTACGGAAATCAACGGTAATAACGGGAAAGTTATTCAGGACGGCGATCTGGATTTCATCGGCGGC‑GGTCACGGTATTGATATCACCGGTGACAg                                                                                                                                                <  1:130907/149‑1 (MQ=255)      aaTGACACAATAAACAACAATGGCAAAACCACCGTGGACGGTAAAGATTCCACCGGTACGGAAATCAACGGTAGTAACGGGAAAGTGATTCATGACGGCGATCTGGATGTCAGCGGCGGC‑GGTCACGGTATTGATATCACCGGTGACAg                                                                                                                                                <  2:469028/149‑1 (MQ=17)         gCCACAGTAAACAACAATGGCAAAACCACCGTTGACGGTAAAGATTCCACCGGTACGGAAATCAACGGTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGC‑GGTCACGGTATTGATATCACCGGCGACAgcgc                                                                                                                                             >  1:106903/1‑149 (MQ=255)           cacaGTAAACAACAATGGCAAAACCACCGTTGACGGTAAAGATTCCACCGGGACGGAAATAAACGGTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTGAGCGGCGGC‑GGTCACGGAATAGATATCACCGGCGACAGCGCGa                                                                                                                                           >  2:612044/1‑149 (MQ=14)                  aacaacAATGGCAAAACCACCGTTGACGGTAAAGATTCCACCGGTACGGAAATCAACGGTAATAACGGAAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGC‑GGTCACGGTATTGATATCACCGGCGACAGCGCGACGggggg                                                                                                                                    >  2:254863/1‑148 (MQ=255)                  aaaaacagTGGCAAAACCACCGTTGACGGTAAAGATTCCACCGGTACCGAAATCAACGGTAATAACGGGAAAGTTATTCAGGACGGCGATCTGGATGTCAGCGGCGGC‑GGTCACGGTATTGATATCACCGGCGACAGCACAACGGTGGa                                                                                                                                    <  2:178962/146‑1 (MQ=11)                     aacaaTGGCAAAACCAGCGGTGACGGTAAAGATTCACCCGGTACGGAAATCAACGGTAATAACGGGAAAGTGATTCAGGACTGCGATCTGGACGTCAGCGGCGGC‑GGTCAAGGTATTGATATCACCTGTCACAGCGCGACGGTTGATaa                                                                                                                                 <  2:493590/149‑1 (MQ=17)                       caaTGGCAAAACCACCGTTGACGGTAAAGATTCCACCGGTACGGAAATCAACGGTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGC‑GGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATcaca                                                                                                                               >  1:214739/1‑149 (MQ=255)                          tGGCAAAACCACCGTTGACGGTAAAGATTCCACCGGTACGGAAATCAACGGTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGC‑GGTCACGGTATTGATATCACCGGCGACAGCGCAACGGTGGATAACAAgg                                                                                                                            <  2:106903/149‑1 (MQ=19)                          tGGCAAAACCACCGTTGACGGGAAAGATTCCACCGGTACGGAAATCAACGGTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGC‑GGTCACGGTGTTGATATCACCGGTGACAGCGCGACGGTGGATAACAAgg                                                                                                                            <  1:338709/149‑1 (MQ=255)                            tgaaaaCCACCGTTGACGGTAAAGATTACACCGGTACGGAAATCAACGGTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGC‑GGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGc                                                                                                                          <  2:163645/147‑1 (MQ=255)                                 accaccGTTGACGTTAAAGATTCCACCAGTACGGAAAACAAGAGTGGGAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGC‑GGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCACCAt                                                                                                                     <  1:289698/149‑1 (MQ=14)                                   caccGTTGACGGTAAAGATTCCACCGGTACGGAAATCAACGGTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGC‑GGTCACGGTATTGATATCACCGGCGACAGCGCAACGGTGGATAACAAGGGCACCATGa                                                                                                                   <  2:35520/149‑1 (MQ=18)                                      cGTTGACGGTAAAGATTCCACCGGTACGGAAATCAACGGTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGC‑GGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCACCATGACCg                                                                                                                <  1:496476/149‑1 (MQ=255)                                          gACGGTAAAGATTCCACCGGTACGGAAATCAACGGTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGC‑GGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCACCATGACCGTCAc                                                                                                            <  1:618080/149‑1 (MQ=255)                                            cGGTAAAGATTCCACCGGTACGGAAATCAACGGTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGC‑GGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCACCATGACCGTCACCg                                                                                                          <  1:598432/149‑1 (MQ=255)                                               tAAATAGTCCACCGGTACGGAAATCAACGGTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGC‑GGTCACGGTATTGATAGCACCGGTGACAGCGCGACGGTGGATAACAAGGGCACCATGACCGTCACCGATc                                                                                                       <  2:267957/149‑1 (MQ=255)                                                   gATTCCACCGGGACGGAAATCAACGGTAATAACGGGAAAGTGATTCATGACGGCGATCTGGATGTCAGCGGCGGC‑GGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGa                                                                                                   <  1:16481/149‑1 (MQ=255)                                                        cACCGGTACGGAAATCAACGGTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGATGCCAGCGGCGGC‑GGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCa                                                                                              <  2:419351/149‑1 (MQ=255)                                                          ccGGTACGGAAATCAACGGTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGC‑GGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATg                                                                                            <  1:312636/149‑1 (MQ=255)                                                                                  cgggcaaaTTGGTTCAGGACGGGGGTCTGGATGTCAGCGGTGGC‑GGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTCGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAg                                                                    <  2:330569/144‑1 (MQ=14)                                                                                   cGGGAAAGGGATTCAGGACGTCCATCTGTTTGTCATCGGCGGC‑GCGCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGACAACAAGCGCACCATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAgg                                                                   <  2:367429/149‑1 (MQ=17)                                                                                        aaGTGATTCAGGACTGCGATCTTGCTGTCAGCGGCGGC‑GGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCATc                                                              <  2:179848/149‑1 (MQ=255)                                                                                             aTTCAGGACGGCGATCAGATTGACAGC‑GCGTCGGGTCGCGGTATTGAGATCAGCGGCGACAGCGCCACGGTGGATGACAAAGGCTCAATGACCGTCACCGATCCGGAGCCCATAGGTATCCAGATCGACGGTGACAAGGCAATCGTCaa                                                         >  2:547244/1‑149 (MQ=2)                                                                                                      ggCGATCTGGATGTCAGCGGCGGC‑GGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCCCCATGACCGTCACCGATCCGGAGTCCATCGGTATCCAGATCGACGGCGACAAGGCCATCGTCAACAACGAAgg                                                >  2:181514/1‑149 (MQ=255)                                                                                                         gATCTGGATGTCAGCGGCGGC‑GGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCATCGTCAATAACGAAGGCga                                             >  1:657519/1‑149 (MQ=255)                                                                                                                aTGTCAGCGGCGGC‑GGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCATCGTCAATAACGAAGGCGAGAGCAcc                                      <  1:445291/149‑1 (MQ=255)                                                                                                                        ggcggc‑ggTCACGGTATTGATATCACCGGTGACAGCGAGACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCAGCGTCAATAACGAAGGCGAGAGCACCATCACCaa                              <  1:334911/149‑1 (MQ=255)                                                                                                                         gcggc‑ggTCACGGTATTGATATCACCGGTAACAGCGCGACGGTGGATAACAAGGACACCATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCATCGTCAATAACGAAGGCGAGAGCACCATCACCAAc                             <  1:572794/149‑1 (MQ=255)                                                                                                                                         ttGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTTCATGGGTATCCTGATTGACGGTGACAAGGCCATCGTCAATAACGAAGGCGAGGGTACCATCACCAACGGTggcaccggcacc              <  1:260172/149‑1 (MQ=17)                                                                                                                                                  ccGGTGACAGCGCGACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCATCGTCAATAACGAAGGCGAGAGCACCATCACCAACGGTGGCACCGGCACCCAGATTAAt     <  2:214739/149‑1 (MQ=255)                                                                                                                                                     gTGACAGCGCGACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCATCGTCAATAACGAAGGCGAGAGCACCATCACCAACGGTGGCACCGGCACCCAGATTAATGGt  <  1:337207/149‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                                    GTGATAATGCCACAGTAAACAACAATGGCAAAACCACCGTTGACGGTAAAGATTCCACCGGTACGGAAATCAACGGTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGC‑GGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCATCGTCAATAACGAAGGCGAGAGCACCATCACCAACGGTGGCACCGGCACCCAGATTAATGGT  >  NC_000913_3_hsa_pgi/1466053‑1466348

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑