Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913_3_hsa_tpiA 1,632,949 C→T 11.0% intergenic (‑664/‑123) ydfJ ← / → ydfK pseudogene, MFS transporter family; interrupted by Qin prophage;Phage or Prophage Related; putative transport protein/cold shock protein, function unknown, Qin prophage

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913_3_hsa_tpiA1,632,9490CT11.0% 120.7 / 6.9 46intergenic (‑664/‑123)ydfJ/ydfKpseudogene, MFS transporter family; interrupted by Qin prophage;Phage or Prophage Related; putative transport protein/cold shock protein, function unknown, Qin prophage
Reads supporting (aligned to +/- strand):  ref base C (25/15);  new base T (2/3);  total (28/18)
Fisher's exact test for biased strand distribution p-value = 3.75e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.01e-01

GACAATGTTTATCTACGAACTTTAAGAACACCCAAGATAAAAATTGTCAACTATATCATATATAACACATTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCCCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTGAATCAGACATACAATATCGCAATGAAAATCAATAATATTTTAAGGAATATCTTCATGAAATCAAAAGACACCC  >  NC_000913_3_hsa_tpiA/1632803‑1633090
                                                                                                                                                  |                                                                                                                                             
gACAATGTTTATCTACGAACTTTAAGAACACCCAAGATAAAAATTGTCAACTATATCATATATAACACATTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCta                                                                                                                                            >  2:422340/1‑150 (MQ=25)
 aCAATGTTTATCTACGAACTTTAAGAACACCCAAGATAAAAATTGTCAACTATATCATATATAACACATTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCCCtaa                                                                                                                                           >  1:276223/1‑150 (MQ=255)
         tATCTACGAACTTTAAGAACACCCAAGATAAAAATTGTCAACTATATCATATATAACACATTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCCCTAATAAAATTa                                                                                                                                   >  1:233768/1‑150 (MQ=255)
              aCGAACTTTAAGAACACCCAAGATAAAAATTGTCAACTATATCATATATAACACATTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCCCTAATAAAATTAGGGAt                                                                                                                              <  4:33091/150‑1 (MQ=255)
                gAACTTTAAGAACACCCAAGATAAAAATTGTCAACTATATCATATATAACACATTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCACTAATAAAATTAGGGATTg                                                                                                                            >  4:378696/1‑150 (MQ=38)
                   cTTTAAGAACACCCAAGATAAAAATTGTCAACTATATCATATATAACACATTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCCCTAATAAAATTAGGGATTGGCa                                                                                                                         >  3:384238/1‑150 (MQ=255)
                    tttAAGAACACCCAAGATAAAAATTGTCAACTATATCATATATAACACATTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCCCTAATAAAATTAGGGATTGGCat                                                                                                                        >  2:164946/1‑150 (MQ=39)
                          aaCACCCAAGATAAAAATTGTCAACTATATCATATATAACACATTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCCCTAATAAAATTAGGGATTGGCATATCCaa                                                                                                                  >  2:4567/1‑150 (MQ=255)
                           acacCCAAGATAAAAATTGTCAACTATATCATATATAACACATTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCCCTAATAAAATTAGGGATTGGCATATCCAAt                                                                                                                 >  4:266916/1‑150 (MQ=40)
                              cccAAGATAAAAATTGTCAACTATATCATATATAACACATTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCCCTAATAAAATTAGGGATTGGCATATCCAATAAc                                                                                                              <  2:564791/150‑1 (MQ=40)
                                    aTAAAAATTGTCAACTATATCATATATAACACATTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCCCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGAc                                                                                                        >  3:247452/1‑150 (MQ=37)
                                     tAAAAATTGTCAACTATATCATATATAACACATTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACa                                                                                                       <  3:256552/150‑1 (MQ=17)
                                       aaaaTTGTCAACTATATCATATATAACACATTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCCCTAATAAAATTAGGGATTGGCATATCCAATAACCcaaacaaa                                                                                                     >  4:31840/1‑150 (MQ=38)
                                        aaaTTGTCAACTATATCATATATAACACATTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCCCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACaaaa                                                                                                    <  2:178578/150‑1 (MQ=39)
                                                aaCTATATCATATATAACACATTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCCCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGta                                                                                            >  2:48788/1‑150 (MQ=38)
                                                   tataTCATATATAACACATTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCCCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATaa                                                                                         >  3:155891/1‑150 (MQ=38)
                                                    atatCATATATAACACATTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCCCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAg                                                                                        <  3:178084/150‑1 (MQ=39)
                                                         atatatAACACATTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCCCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAAc                                                                                   <  4:302916/150‑1 (MQ=38)
                                                             ataACACATTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCCCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACatat                                                                               >  1:222200/1‑150 (MQ=39)
                                                             ataACACATTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCCCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACatat                                                                               <  4:323039/150‑1 (MQ=38)
                                                              taACACATTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCCCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATc                                                                              >  4:169500/1‑150 (MQ=39)
                                                               aaCACATTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCCCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATcc                                                                             <  2:428740/150‑1 (MQ=38)
                                                               aaCACATTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCCCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATcc                                                                             <  4:114350/150‑1 (MQ=38)
                                                                acacATTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCt                                                                            <  1:422340/150‑1 (MQ=17)
                                                                acacATTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCt                                                                            <  3:371951/150‑1 (MQ=14)
                                                                    aTTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCCCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTGAAt                                                                        >  1:394192/1‑150 (MQ=39)
                                                                    aTTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCCCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTGAAt                                                                        >  1:555158/1‑150 (MQ=39)
                                                                     ttACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCTCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTGAATc                                                                       >  2:141570/1‑150 (MQ=17)
                                                                        cTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCCCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTTAATCAGa                                                                    <  2:587271/150‑1 (MQ=38)
                                                                            ttCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCCCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTGAATCAGACATa                                                                >  1:570224/1‑150 (MQ=39)
                                                                              cGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCCCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTGAATCAGACATACa                                                              <  2:174070/150‑1 (MQ=38)
                                                                                          aaCAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCCCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTGAATCAGACATACAATATCGCAATgc                                                  <  2:261985/150‑2 (MQ=37)
                                                                                               cATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCCCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTGAATCAGACATACAATATCGCAATGAAAATc                                             >  4:227763/1‑150 (MQ=37)
                                                                                                           cacaTCTCTCCTTATCATATTCAGCATTTTTAGTCATGCCCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTGAATCAGACATACAATATCGCAATGAAAATCAATAATATTTTa                                 >  1:25391/1‑150 (MQ=38)
                                                                                                            acaTCTCTCCTTATCATATTCAGCATTTTTAGTCATGCCCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTGAATCAGACATACAATATCGCAATGAAAATCAATAATATTTTaa                                >  2:270695/1‑150 (MQ=37)
                                                                                                            acaTCTCTCCTTATCATATTCAGCATTTTTAGTCATGCCCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTGAATCAGACATACAATATCACAATGAAAATCAATAATATTTTaa                                >  2:9006/1‑150 (MQ=38)
                                                                                                                   tcCTTATCATATTCAGCATTTTTAGTCATGACCGAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTGAAGCAGACATACAATATCGCAATGAAAATCAATAATATTTTAAGGAatat                         <  3:31840/150‑1 (MQ=12)
                                                                                                                     cTTATCATATTCAGCATTTTTAGTCATGCCCCAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTGAATCAGACATACAATATCGCAATGAAAATCAATAATATTTTAAGAAATATCt                       >  2:275737/1‑150 (MQ=17)
                                                                                                                        aTCATATTCAGCATTTTTAGTCATGCCCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTGAATCAGACATACAATATCGCAATGAAAATCAATAATATTTTAAGGAATAAATTCa                    >  1:302276/1‑150 (MQ=17)
                                                                                                                         tCATATTCAGCATTTTTAGTCATGCCCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTGAATCAGACATACAATATCGCAATGAAAATCAATAATATTTTAAGGAATATCTTCAt                   >  4:368784/1‑150 (MQ=32)
                                                                                                                           atatTCAGCATTTTTAGTCATGCCCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTGAATCAGACATACAATATCGCAATGAAAATCAATAATATTTTAAGGAATATCTTCATGa                 <  1:521502/150‑1 (MQ=32)
                                                                                                                              ttCAGCATTTTTAGTCATGCCCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTGAATCAGACATACAATATCGCAATGAAAATCAATAATATTTTAAGGAATATCTTCATGAAAt              >  1:326337/1‑150 (MQ=32)
                                                                                                                              ttCAGCATTTTTAGTCATGCCCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTGAATCAGACATACAATATCGCAATGAAAATCAATAATATTTTAAGGAATATCTTCATGAAAt              >  4:129926/1‑150 (MQ=32)
                                                                                                                                      ttttAGTCATGCCCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATACCCTGAATCAGACATACAATATCGCAATGAAAATCAATAATATTTTAAGGAATATCTTCATGAAATCAAAAGac      <  3:342329/150‑1 (MQ=17)
                                                                                                                                        ttAGTCATGCCCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTGAATCAGACATACAATATCGCAATGAAAATCAATAATATTTTAAGGAATATCTTCATGAAATCAAAAGacac    <  1:164946/150‑1 (MQ=32)
                                                                                                                                          aGTCATGCCCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTGAATCAGACATACAATATCGCAATGAAAATCAATAATATTTTAAGGAATATCTTCATGAAATCAAAAGACAccc  >  4:257853/1‑150 (MQ=32)
                                                                                                                                                  |                                                                                                                                             
GACAATGTTTATCTACGAACTTTAAGAACACCCAAGATAAAAATTGTCAACTATATCATATATAACACATTACTAATTCGAGGCTATATGAACAGCATACTGATAATCACATCTCTCCTTATCATATTCAGCATTTTTAGTCATGCCCTAATAAAATTAGGGATTGGCATATCCAATAACCCAGACAAAACCGATGTATAAGTCAACATATCCTGAATCAGACATACAATATCGCAATGAAAATCAATAATATTTTAAGGAATATCTTCATGAAATCAAAAGACACCC  >  NC_000913_3_hsa_tpiA/1632803‑1633090

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑