Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_hsa_tpiA	1,202,211	C→T	intergenic (‑127/+48)	ymfJ ← / ← cohE	e14 prophage; uncharacterized protein/e14 prophage; repressor protein phage e14

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_hsa_tpiA	1,202,211	0	C	T	100.0%	113.2 / NA	36	intergenic (‑127/+48)	ymfJ/cohE	e14 prophage; uncharacterized protein/e14 prophage; repressor protein phage e14
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (15/21);  total (15/21)

TTCAAATTCTGCTCATTCATCTATTCTCTCCACTGAAATCATCCGCTAACGAATCATCCCGGTCTTCGTACGTACCGGGCGGGCTACTTCGTGGGCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTACATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAACATTGATTAGGCTTTGATTTTGTATCTTCTTGGTTTTCCTGAGAAAATCACAGTACCAATTATAGAGCAATTACCGTTGATCTTAATGTAAGGCTCAG  >  NC_000913_3_hsa_tpiA/1202065‑1202350                                                                                                                                                   |                                                                                                                                            ttCAAATTCTGCTCATTCATCTATTCTCTCCACTGAAATCATCCGCTAACGAATCATCCCGGTCTTCGTACGTACCGGGCGGGCTACTTCGTGGGCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAGAGGTatat                                                                                                                                           >  2:135178/1‑149 (MQ=255) ttCAAATTCTGCTCATTCATCTATTCTCTCCACTGAAATCATCCGCTAACGAATCATCCCGGTCTTCGTACGTACCGGGCGGGCTACTTCGTGGGCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTatat                                                                                                                                           >  1:221984/1‑149 (MQ=255)     aaTTCTGCTCATTCATCTATTCTCTCCACTGAAATCATCCGCTAACGAATCATCCCGGTCTTCGTACGTACCGGGCGGGCTACTTCGTGGGCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTc                                                                                                                                       <  1:202231/149‑1 (MQ=255)               attcatCTATTCTCTCCACTGAAATCATCCGCTAACGAATCATCCCGGTCTTCGTACGTACCGGGCGGGCTACTTCGTGGGCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATaaaa                                                                                                                             >  2:327658/1‑149 (MQ=255)                  catCTATTCTCTCCACTGAAATCATCCGCTAACGAATCATCCCGGTCTTCGTACGTACCGGGCGGGCTACTTCGTGGGCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATaaaaaaa                                                                                                                          <  1:82903/149‑1 (MQ=255)                             tcCACTGAAATCATCCGCTAACGAATCATCCCGGTCTTCGTACGTACCGGGCGGGCTACTTCGTGGTCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCCAAGGTATATTGTCCAGTATAAAAAACCCTTCCGAAGc                                                                                                               >  2:535995/1‑149 (MQ=255)                                aCTGAAATCATCCGCTAACGAATCATCCCGGTCTTCGTACGTACCGGGCGGGCTACTTCGTGGGCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAgg                                                                                                            >  1:499871/1‑149 (MQ=255)                                         atcCGCTAACGAATCATCCCGGTCTTCGTACGTACCGGGCGGGCTACTTCGTGGGCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAAc                                                                                                   <  1:480914/149‑1 (MQ=255)                                         atcCGCTAACGAATCATCCCGGTCTTCGTACGTACCGGGCGGGCTACTTCGTGGGCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTAATAAAc                                                                                                   >  1:529406/1‑149 (MQ=255)                                           ccGCTAACCAATCATCCCGGTCTTCGTACGTACCGGGCGGGCTACTTCGTGGGCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAACAt                                                                                                 <  1:154256/149‑1 (MQ=255)                                                  cGAATCATCCCGGTCTTCGTACGTACCGGGCGGGCTACTTCGTGGGCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAACATTGATTAg                                                                                          <  1:239846/149‑1 (MQ=255)                                                   gAATCATCCCGGTCTTCTTACGTACCGGGCGGGCTACTTCGTGGGCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAACATTGATTAgg                                                                                         >  1:88531/1‑149 (MQ=255)                                                   gAATCATCCCGGTCTTCGTAAGTACCGGGGGGGCTAATTCGCGGGCGTCCTGCCTGTTTTTTGTTTATCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAATTCCTGCCGAAGCAGGTTCATAAACATTGATTAgg                                                                                         <  2:566414/149‑1 (MQ=255)                                                            cGGTCTTCGTACGTACCGGGCGGGCTACTTCGTGGGCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAACATTGATTAGGCTTTGAttt                                                                                >  2:429119/1‑149 (MQ=255)                                                              gTCTTCGTACGTACCGGGCGGGCTACTTCGTGGGCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTAAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAACATTGATTAGGCTTTGATTTTg                                                                              <  2:173953/149‑1 (MQ=255)                                                                 ttCGTACGTACCGGGCGGGCTACTTCGTGGGCGTCCTGCCTGTTTGTTATTTCTCTTGGGTACATTATGTGTCTCAAAGGTATATTGTCAAGTAGAAAAAAATCTGCCGAAGCAGGTTCATAAACATTGATTAGGCTTTGATTTTGTAt                                                                           >  2:155152/1‑149 (MQ=255)                                                                         tacCGGGCGGGCTACTTCGTGGGCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAACATTGATTAGGCTTTGATTTTGTATCTTCTTgg                                                                   <  1:271957/149‑1 (MQ=255)                                                                                ctgggtACTTCGGTGGCGGCCTGGCTGTTTGTTGTTTCTCGTGTGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAACACCTGCCGAAGCAGGTTCATACACATTGATTAGGCTTTGATTTTGTATCTTCTTGGTTTTCCt                                                            <  2:84378/144‑1 (MQ=255)                                                                                     tACTTCGTGGGCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAACATTGATTAGGCTTTGATTTTGTATCTTCTTGGTTTTCCTGAGaa                                                       >  1:196743/1‑149 (MQ=255)                                                                                            tGGGCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAACATTGATTAGGCTTTGATTTTGTATCTTCTTGGTTTTCCTGAGAAAATcaca                                                <  1:516322/149‑1 (MQ=255)                                                                                             gggCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGc                                                                                                                     <  1:147189/79‑1 (MQ=255)                                                                                             gggCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGc                                                                                                                     >  2:147189/1‑79 (MQ=255)                                                                                               gCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAACATTGATTAGGCTTTGATTTTGTATCTTCTTGGTTTTCCTGAGAAAATCACAGTa                                             <  1:516732/149‑1 (MQ=255)                                                                                                    ctgcctgTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAACATTGATTAGGCTTTGATTTTGTATCTTCTTGGTTTTCCTGAGAAAATCACAGTaactat                                        >  2:227927/1‑144 (MQ=255)                                                                                                    ctgcctgTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGAAAAATATAAAAAAACCTGCCGAAGCAGGTTCATAAACATTGATTAGGCTTTGATTTTGTATCTTCTTGGTTTTCCTGAGAAAATCACAGTACCAAt                                        <  2:491000/149‑1 (MQ=255)                                                                                                           tttgttGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAACATTGATTAGGCTTTGATTTTGTATCTTCTTGATTTTCCTGAGAAAATTACAGTCCCAATtatatga                                 >  2:17231/1‑146 (MQ=255)                                                                                                           tttgttGTTTCTATCGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATCAATATACCTACTGAAGCCGGTTCATAAAACTTGCTTAGGATTTGATTTTGTATCTCCTTGATTTTCCTGAGAAAATCACAGTAACAATTTTagag                                 >  2:277539/1‑149 (MQ=255)                                                                                                            tggtttttTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATATAAACACCTGCCGAAGCAGTTTCATATACATTGATTAGGCTTTGATTTTGTATTTTCTGGGTTTTCCTGAGAAAATTATAGTACAAATTATAGAGc                                <  2:138389/147‑1 (MQ=255)                                                                                                                tgttTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAACATTGAt                                                                                             >  2:173072/1‑84 (MQ=255)                                                                                                                tgttTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAACATTGAt                                                                                             <  1:173072/84‑1 (MQ=255)                                                                                                                 gttTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAACATTGATTAGGCTTTGATTTTGTAGCTTCTTGGTTTTCCTGAGAAAATCACAGTACCAATTATAGAGCAATTa                           >  1:233370/1‑149 (MQ=255)                                                                                                                     ctctCGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAACATTGATTAGGCTTTGATTTTGTATCTTCTTGGTTTTCCTGAGAAAATCACAGTACCAATTATAGAGCAATTACCGt                       <  1:301938/149‑1 (MQ=255)                                                                                                                      tctTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAACATTGATTAGGCTTTGATTTTGTATCTTCTTGGTTTTCCTGAGAAAATCACAGTACCAATTATAGAGCAATTACCGtt                      <  1:219395/149‑1 (MQ=255)                                                                                                                               cATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAACATTGATTAGGCTTTGATTTTGTATCTTCTTGGTTTTCCTGAGAAAATCACAGTACCAATTATAGAGCAATTACCGTTGATCttttg             >  1:136013/1‑146 (MQ=255)                                                                                                                                   aTGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAACATTGATTAGGCTTTGATTTTGTATCTTCTTGGTTTTCCTGAGAAAATCACAGTACCAATTATAGAGCAATTACCGTTGATCTTAATGTaa         <  1:429119/149‑1 (MQ=255)                                                                                                                                          tcAAATGTATAGTGTCAAGTATAAAACATCCTGCCGAAGCAGGTTCATAAACATTGATTAGGCTTTGATTTTGTATCTTCTTGGTTTTCCTGAGAAAATCACAGTACCAATTATAGAGCAATTACCGTTGATCTTAATGTAAGGCTCAg  <  2:269679/149‑1 (MQ=255)                                                                                                                                          tcAAAGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAACATTGATTAGGCTTTGATTTTGTATCTTCTTGGTTTTCCTGAGAAAATCACAGTACCAATTATAGCGCATTTACCGTTGATCTTAATGTAAGGCTCAg  <  1:327658/149‑1 (MQ=255)                                                                                                                                          gcAAAGGTATATTGACAAGTATAAAAAAACGTGTCGAAGCAGTTTCATAATCATTGATTAGGCTGTGATTTTGTATCTTCTTGGTTTTCCTGAGAAAATTACAGTACCAATTGTAGAGCAATTAGCGTTGATCTTAATGTAAGGGTCAg  <  2:451286/148‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                            TTCAAATTCTGCTCATTCATCTATTCTCTCCACTGAAATCATCCGCTAACGAATCATCCCGGTCTTCGTACGTACCGGGCGGGCTACTTCGTGGGCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTACATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAACATTGATTAGGCTTTGATTTTGTATCTTCTTGGTTTTCCTGAGAAAATCACAGTACCAATTATAGAGCAATTACCGTTGATCTTAATGTAAGGCTCAG  >  NC_000913_3_hsa_tpiA/1202065‑1202350

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑