Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,207,981	G→A	A161T (GCC→ACC)	stfP →	e14 prophage; uncharacterized protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,207,981	0	G	A	97.5%	259.9 / ‑2.1	79	A161T (GCC→ACC)	stfP	e14 prophage; uncharacterized protein
Reads supporting (aligned to +/- strand):  ref base G (1/1);  new base A (41/36);  total (42/37)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.24e-01

GCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATGCCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATACAACCACTTCGTTTTTATTACGGT  >  NC_000913/1207884‑1208077                                                                                                  |                                                                                                 gCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATAcc                                                                                                <  1:1478632/100‑1 (MQ=255) gCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATAcc                                                                                                <  1:1477539/100‑1 (MQ=255)  cAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCt                                                                                               >  1:669286/1‑100 (MQ=255)      cAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTgtgt                                                                                           >  1:642974/1‑100 (MQ=255)       aGTAATCGTTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGtt                                                                                          >  2:1027190/1‑100 (MQ=255)       aGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGtt                                                                                          >  2:839822/1‑100 (MQ=255)        gTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTg                                                                                         <  2:726091/100‑1 (MQ=255)              aTTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCgttg                                                                                   >  2:1032015/1‑100 (MQ=255)              aTTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCgttg                                                                                   >  2:1924516/1‑100 (MQ=255)                tCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATGCCTGTGTTGCCgttgtt                                                                                 >  1:1149048/1‑100 (MQ=255)                 cAGTGGGGGTGGAATGCCGCAAATGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGttgttg                                                                                <  1:1223102/100‑1 (MQ=255)                 cAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGttgttg                                                                                <  1:1208871/100‑1 (MQ=255)                  ngTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCAGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGc                                                                               >  2:694244/2‑100 (MQ=255)                  aGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGc                                                                               <  1:1390068/100‑1 (MQ=255)                  aGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGc                                                                               <  1:1105721/100‑1 (MQ=255)                   gTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCa                                                                              >  2:475045/1‑100 (MQ=255)                     gggggTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCaaa                                                                            >  1:1524195/1‑100 (MQ=255)                     gggggTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCaaa                                                                            <  1:1932785/100‑1 (MQ=255)                      ggggTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAAt                                                                           >  1:151379/1‑100 (MQ=255)                       gggTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAAtt                                                                          >  1:6736/1‑100 (MQ=255)                        ggTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTa                                                                         <  2:1210057/100‑1 (MQ=255)                        ggTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTa                                                                         <  2:1524203/100‑1 (MQ=255)                            gAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGan                                                                     <  2:433600/100‑2 (MQ=255)                            gAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGAc                                                                     <  2:1219561/100‑1 (MQ=255)                             aaTGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACa                                                                    <  1:977248/100‑1 (MQ=255)                             aaTGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACa                                                                    >  1:769125/1‑100 (MQ=255)                              aTGCCGCAAAAGCATCTGCCTCTGGAGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACaa                                                                   >  1:611090/1‑100 (MQ=255)                               tGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAAt                                                                  >  2:1354214/1‑100 (MQ=255)                                gCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATg                                                                 <  2:1241460/100‑1 (MQ=255)                                 ccGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGt                                                                >  1:1180331/1‑100 (MQ=255)                                  cGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTTCCGGTTACGGTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATTACAATGt                                                                >  1:838811/1‑99 (MQ=255)                                    cAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAg                                                             <  1:386204/100‑1 (MQ=255)                                    cAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAg                                                             <  2:1072752/100‑1 (MQ=255)                                     aaaaGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAgc                                                            <  2:1349947/100‑1 (MQ=255)                                       aaGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAgcgc                                                          >  2:431472/1‑100 (MQ=255)                                           aTCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCt                                                      >  1:1826406/1‑100 (MQ=255)                                            tCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTa                                                     >  2:756966/1‑100 (MQ=255)                                              tGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATc                                                   >  2:1197635/1‑100 (MQ=255)                                              tGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATc                                                   >  1:676696/1‑100 (MQ=255)                                               gCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCa                                                  >  1:133942/1‑100 (MQ=255)                                               gCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCa                                                  >  1:1229910/1‑100 (MQ=255)                                                 ctctGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAAt                                                >  2:1063935/1‑100 (MQ=255)                                                 ctctGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAAt                                                >  2:118844/1‑100 (MQ=255)                                                  tctGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATg                                               <  1:1282997/100‑1 (MQ=255)                                                      ggggggATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGt                                           <  2:554778/100‑1 (MQ=255)                                                        ggggATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTgg                                         <  2:1525741/100‑1 (MQ=255)                                                          ngATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCa                                       >  1:338903/2‑100 (MQ=255)                                                          ggATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCa                                       >  2:899160/1‑100 (MQ=255)                                                          ggATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCa                                       <  2:977008/100‑1 (MQ=255)                                                           gATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCaa                                      >  1:551967/1‑100 (MQ=255)                                                              ggAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACgg                                   >  1:1221762/1‑100 (MQ=255)                                                                  aTACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACgggggg                               >  1:437215/1‑100 (MQ=255)                                                                  aTACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACgggggg                               <  1:457625/100‑1 (MQ=255)                                                                       gTTGTATTCCCGGTTGCGTTTAATAATGCCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGAtata                          <  1:405128/100‑1 (MQ=255)                                                                       gTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGAtata                          >  2:734099/1‑100 (MQ=255)                                                                       gTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGAAAATGTCAGCGCACCTATAAATGCAGTGGAAACGGGGGGAtata                          >  1:438720/1‑100 (MQ=255)                                                                        ttGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATAc                         >  1:463348/1‑100 (MQ=255)                                                                          gTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATACaa                       >  2:1333652/1‑100 (MQ=255)                                                                           tATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATACAAc                      <  2:838812/100‑1 (MQ=255)                                                                           tATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATACAAc                      >  2:415261/1‑100 (MQ=255)                                                                              tCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATACAACCAc                   <  2:1180333/100‑1 (MQ=255)                                                                                  ggTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATACAACCACTTCg               <  2:521641/100‑1 (MQ=255)                                                                                   gTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATACAACCACTTCGt              <  2:653824/100‑1 (MQ=255)                                                                                    ttGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATACAACCACTTCGtt             <  2:611092/100‑1 (MQ=255)                                                                                    gtGCGTGTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAAGGGCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATACAACCACTTCg               <  1:861762/97‑1 (MQ=255)                                                                                     tGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATACAACCACTTCGttt            >  2:1815334/1‑100 (MQ=255)                                                                                     tGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATACAACCACTTCGttt            <  2:865543/100‑1 (MQ=255)                                                                                       cGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGTAGTGGCAACGGGGGGATATACAACCACTTCGttttt          <  1:718916/100‑1 (MQ=255)                                                                                       cGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATACAACCACTTCGttttt          <  1:1197633/100‑1 (MQ=255)                                                                                       cGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATACAACCACTTCGttttt          <  2:151380/100‑1 (MQ=255)                                                                                       cGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATACAACCACTTCGttttt          >  2:675722/1‑100 (MQ=255)                                                                                       cGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATACAACCACTTCGttttt          >  1:1877153/1‑100 (MQ=255)                                                                                        gTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATACAACCACTTCGTTTtta         <  2:1826418/100‑1 (MQ=255)                                                                                        gTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATACAACCACTTCGTTTtta         >  1:1679538/1‑100 (MQ=255)                                                                                         tttAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATACAACCACTTCGTTTttat        <  1:1007291/100‑1 (MQ=255)                                                                                          ttAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATACAACCACTTCGTTTttat        >  2:1894419/1‑99 (MQ=255)                                                                                            aataatACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATACAACCACTTCGTTTttattan     <  2:338905/100‑2 (MQ=255)                                                                                             ataataCCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATACAACCACTTCGTTTTTATTACg    <  1:899159/100‑1 (MQ=255)                                                                                             ataataCCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATACAACCACTTCGTTTTTATTACg    <  2:1154918/100‑1 (MQ=255)                                                                                              taatACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATACAACCACTTCGTTTTTATTACgg   <  1:1010199/100‑1 (MQ=255)                                                                                               aatACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATACAACCACTTCGTTTTTATTACGGt  >  1:746840/1‑100 (MQ=255)                                                                                                  |                                                                                                 GCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATGCCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATACAACCACTTCGTTTTTATTACGGT  >  NC_000913/1207884‑1208077

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