Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913_3_hsa_tpiA	1,466,438	T→G	18.9%	pseudogene (1047/2513 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_tpiA	1,466,438	0	T	G	18.9%	79.8 / 6.2	47	pseudogene (1047/2513 nt)	ydbA	pseudogene, autotransporter homolog; interrupted by IS2 and IS30
Reads supporting (aligned to +/- strand):  ref base T (14/23);  new base G (2/8);  total (16/31)
Fisher's exact test for biased strand distribution p-value = 4.57e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACGAAGGCGAGAGCACCATCACCAACGGTGGCACCGGCACCCAGATTAATGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATCAACGGTAATAACGGAAAAGTTATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGCGACAGCGCAACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATCGGTATCCAGGTTGACGGCGACCAGGCGGTTGTT  >  NC_000913_3_hsa_tpiA/1466296‑1466585                                                                                                                                               |                                                                                                                                                    aCGAAGGCGAGAGCACCATCACCAACGGTGGCACCGGCACCCAGATTAAGGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATCAACGGTAATAACGGACAAGTTATTCAg                                                                                                                                               <  1:514319/149‑1 (MQ=255)          agagCACCATCACTAACGATGACACCTACACCCAGATTAAGGGTGATTACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGTAAGGATTCCACCGGTACGGAAATCAACGGTAATAACGGAAAAGTTATTTAGGACGGCGAt                                                                                                                                      <  2:431549/149‑1 (MQ=17)                         aCGGTGGCACCGGCACCCAGATTAATGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATCAACGGTAATAACGGAAAAGTTATTCAGGACGGCGATCTGGATGTCAgcggc                                                                                                                       >  2:458407/1‑149 (MQ=255)                                    ggcaccCAGATTAATGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATCAACGGTAATAACGGAAAAGTTATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACgg                                                                                                            <  1:607212/149‑1 (MQ=255)                                    ggcaccCAGATTAAGGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATCAACGGTAATAACGGAAAAGTTATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACgg                                                                                                            <  1:607208/149‑1 (MQ=255)                                      ccctgataTTAAGGGTGATAACGCCACAGTAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATCAACGGTAATAACGGAAAAGTTATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTa                                                                                                          <  2:448930/142‑1 (MQ=11)                                       accCAGATTAATGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATCAACCGTAATAAAAGCAAAGTTATACCGGACGGCGATCTGGATCTCACCGGAGGCGATCACCGtct                                                                                                         >  2:150056/1‑147 (MQ=17)                                          cAGATTAATGGTGAGGACGCCACAGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATCAACGGTAATAACGGAAAAGTTATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGa                                                                                                      <  1:25637/149‑1 (MQ=255)                                                      gaggatgCCACAGTAAAGAACAACGGCAAAAGCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATCAACGGTAATAACGGAAAAGTTATTCAGGACGGCGATCTGGATGTCAGGGGGGGCGGTCACGGTATTGATATCACCGGCGa                                                                                          <  2:389169/143‑1 (MQ=11)                                                       atgaCGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATCAACGGTAATAACGGAAAAGTTATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCg                                                                                              <  1:720918/144‑1 (MQ=255)                                                       atgaCGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATCAACGGTAATAACGGAAAAGTTATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCg                                                                                              >  2:720918/1‑144 (MQ=255)                                                          aCGCCACGGCAAACAACAACGGCAAAACCAACGCTGACGGCAAGGATTCCACCGGTACGGAAATCAACGGTAATAACGGAAAAGTTATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGCGACAgc                                                                                      <  1:650946/149‑1 (MQ=255)                                                          aCGCCACAGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATCAACGGTAATAACGGAAAAGTTATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGCGACAgc                                                                                      <  1:503292/149‑1 (MQ=255)                                                            gCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATCACGGGTAATAACGGAAAAGTTATTAAGGAGGGCGATCTGGAGGTCAGAGGCGCACGTCACGATATTGAGAATACTGGCGACAgagc                                                                                    >  2:479161/1‑149 (MQ=14)                                                                  gCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATCAACGGTAATAACGGAAAAGTTATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGCGACAGCGCAACGGt                                                                              <  1:46763/149‑1 (MQ=255)                                                                  gCAAACAAACACGGCACAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATCAACGGTAATAACGGAAAAGTTATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGCGACAGCGCAACGGt                                                                              <  2:129626/149‑1 (MQ=255)                                                                    aaaCAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATCAACGGTAATAACGGAAAAGGTATTCAGGACGGCGATCTGGATGTCAGCGACGGCGGTCACGGTATTGATATCACCGGCGCCAGCGCCACggctg                                                                            >  2:265175/1‑146 (MQ=14)                                                                      acaacaacGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATCAACGGTAATAACGGAAAAGTTATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGCGACAGCGCAACGGTGGAt                                                                          <  1:758287/149‑1 (MQ=255)                                                                         acaacGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATCAACGGTAATAACGGAAAAGTTATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGCGACAGCGCAACGGTGGATAAc                                                                       <  1:538022/149‑1 (MQ=255)                                                                         acaacGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATCAACGGTAATAACGGAAAAGTTATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGCGACAGCGCAACGGTGGATAAc                                                                       >  2:189790/1‑149 (MQ=255)                                                                         acaacGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATCAACGGTAATAACGGAAAAGTTATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGCCGACAGCGCAACCGTGGATaag                                                                       >  2:83098/1‑148 (MQ=255)                                                                            agggCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATCAACGGTAATAACGGAAAAGTTATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGCGACAGCGCAACGGTGGATAACAAg                                                                    <  2:657315/147‑1 (MQ=255)                                                                             ctgCAAAACCACCGTTGACGGCAAAGATTCCACCGGTACGGAAATCAACGGTAATCCCGGAAAAGTTATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGCGACAGCGCAACGGTGGATAACAAgg                                                                   <  1:276848/147‑1 (MQ=255)                                                                                 aaaaCCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATCAACGGTAATAACGGAAAAGTTATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGGCACGGTATTGATATCCCCGGCGACTGCGCAACGGTGGATAACAAGGGCAc                                                               >  1:694574/1‑149 (MQ=255)                                                                                   aaCCACCGTGGAGGGAAAAGATTCCACCGGGACGGAAATCAACGGTAATAACGGAAAAGTTATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGCGACAGCGCAACGGTGGATAACAAGGGCACCa                                                             <  2:325491/149‑1 (MQ=11)                                                                                    cacaccGTGGACGTCAAAGATGCCACCGGTACGGAAATCAACGGTAATAACGGAAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGCGACAGCGCAACGGTGGATAACAAGGGCACCAt                                                            <  2:257043/147‑1 (MQ=11)                                                                                      caccGTTGACGGCAAGGATTCCACCGGTACGGAAATCAACGGTAATAACGGAAAAGTTATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGGCACGGTATTGATATCACCGGCGACAGCGCACCGGTGGATAACAAGGGCACCATGa                                                          >  1:579327/1‑149 (MQ=255)                                                                                      caccGTTGACGGCAAGGATTCCACAGATGCGGAAATCGTCGTTAAGGACGAAAAAGTTATTCTGGGCGGCGATCTCGGTGTTAGCGGCAGCGGTAACGGTATTGATATCACCGGCGGCACCGCCACGCTGGAGAACAAGGGCACCAtag                                                          >  2:199931/1‑147 (MQ=9)                                                                                                  taaagATTCCACCGGTACGCAAATCAACGGTAATAACGGAAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGCGACAGCGCAACGGTGGATAACAAGGGCACCATGACCGTCACCGATc                                              >  2:708295/5‑149 (MQ=2)                                                                                                   aaGGATTCCACCGGTACGGAAATCAACGGTAATAACGGAAAAGTTATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGCGACAGCGCAACGGTGGATAACAAGGGCACCATGACCGTCACCGATcc                                             >  2:625955/1‑149 (MQ=255)                                                                                                    aGGATTCCACCGGTACGGAAATCAACGGTAATAACGGAAAAGTTATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGCGACAGCGCAACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCg                                            <  1:563779/149‑1 (MQ=255)                                                                                                      gATTCCACCGGTACGGAAATCAACGGTAATAACGGAAAAGTTATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTAt                                                                                                         <  2:781444/86‑1 (MQ=38)                                                                                                       gttCCACCGGTACGGAAATTGAGGGTAATAACGGAAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGCGACAGCGCAACGGTGGATAACAGGGGCACCATGACCGTCACCGATCCGGAg                                         <  2:96703/148‑1 (MQ=11)                                                                                                           cACCGGTACGGAAATCAACGGTAATAACGGAAAAGTTATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGCGACAGCGCAACGGTGGATAACAAGGGCACCATCACCGTCACCGATCCGGAGTCCa                                     >  2:569324/1‑149 (MQ=255)                                                                                                              cGGTACGGAAATCAACGGTAATAACGGAAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGCGACAGCGCAACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATCg                                  <  1:708295/149‑1 (MQ=38)                                                                                                                    ggAAATCAACGGTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGCGACAGCGCAACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATCGGTATcc                            <  2:399628/149‑1 (MQ=17)                                                                                                                    ggAAATCAACGGTAATAACGGAAAAGTTATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGCGACAGCGCAACGGTGGATAACAAGGGCACCATGACCGTCAc                                                   <  2:310182/126‑1 (MQ=255)                                                                                                                    ggAAATCAACGGTAATAACGGAAAAGTTATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGCGACAGCGCAACGGTGGATAACAAGGGCACCATGACCGTCAc                                                   >  1:310182/1‑126 (MQ=255)                                                                                                                     aaaaTCAACGGTAAAAAAGAAAAAGTTATTCACGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGCGACAGCGCAACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATCGGTATCCa                           <  2:193008/148‑1 (MQ=255)                                                                                                                      aagcctccGGTAACAACGGAAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGCGACAGCGCAACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATCGGTATCCAg                          <  2:170324/142‑1 (MQ=255)                                                                                                                      aaaTCAACGGTAATAACGGAAAAGTTATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGCGACAGCGCAACCGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATCGGTATCCAg                          <  1:582779/149‑1 (MQ=255)                                                                                                                        aTCAACGGTAATAACGGAAAAGTTATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGCGACAGCGCAACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATCGGTATCCAGGt                        <  1:458407/149‑1 (MQ=255)                                                                                                                            aCGGTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGTGACAGCGCAACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATCGGTATCCAGGTTGAc                    >  2:393414/1‑149 (MQ=2)                                                                                                                             cGGTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGTGACAGCGCAACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATCGGTATCCAGGTTGACg                   <  2:244878/149‑1 (MQ=16)                                                                                                                                        gAAAAGTTATTCAGGACGGCGATGTGGATGTGAGCGGCGGGGGTCAGGGTATTGATGTCACCGGCGACAGCGCAAGGGTGGATAGCAAGGGAAGCATGACGGTCCGCGATCCGGAGTCCATGGGTATCCAGGTTGATGTCGACCAggtc        >  2:310755/1‑147 (MQ=14)                                                                                                                                           aaGTGATTCAGGACGGCTATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGCGACAGCGCAACGGTGGAGAACAAGGGCCCCATGACCGTCACCGATCCGGAGTCCATCGGTATCCAGGTTGACGGCGACCAGGCGgtt     <  2:465641/149‑1 (MQ=255)                                                                                                                                            aGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGCGACAGCGCAACGGTGGATAACAAGGGCACCCTGACCGTCCACGACCCGGAGTCCCTCGGTATCCAGGTTTTTGGCGACCAGGCGgttg    <  2:198804/149‑1 (MQ=11)                                                                                                                                              ttATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGCGACAGCGCAACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATCGGTATCCAGGTTGACGGCGACCAGGCGgttgtt  <  2:229014/149‑1 (MQ=40)                                                                                                                                               |                                                                                                                                                    ACGAAGGCGAGAGCACCATCACCAACGGTGGCACCGGCACCCAGATTAATGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATCAACGGTAATAACGGAAAAGTTATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGCGACAGCGCAACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATCGGTATCCAGGTTGACGGCGACCAGGCGGTTGTT  >  NC_000913_3_hsa_tpiA/1466296‑1466585

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: ‑