Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 654,252 C→T 58.0% S360L (TCG→TTG)  USA300HOU_RS03120 → Ribonuclease

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE654,2520CT58.0% 15.3 / 39.6 38S360L (TCG→TTG) USA300HOU_RS03120Ribonuclease
Reads supporting (aligned to +/- strand):  ref base C (8/8);  new base T (10/12);  total (18/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.62e-01

TAATGTGTTTATAGAAAATGGTAGTAAATTTGCAAAAGGCGGAAAATACCTAGGTAAAGGTGTTGCTGGTGTAGGATTTGGTATAGGTATGTATGATGACCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTCGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAGCGACTTTTGTTTTAGGAAGTAATCCAGTAGGATGGGTGATTTTAGCAGGTTTGGCTATGAGTACAGTATTTG  >  USA300TCH1516_ALE/654115‑654383
                                                                                                                                         |                                                                                                                                   
taaatggtTTATAGAAAATGGTAGTAAATTTGCAAAAGGCGGAAAATACCTAGGTAAAGGTGTTGCTGGTGTAGGATTTGGTATAGTTCTGTATGATGACCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTCGCa                                                                                                                                  <  1:96460/135‑1 (MQ=255)
             gAAAATGGTAGTAAATTTGCAAAAGGCGGAAAATACCTAGGTAAAGGTGTTGCTGGTGTAGGATTTGGTATAGGTATGTATGATGACCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTCGCATAATGGTATGACg                                                                                                                     <  1:137113/141‑1 (MQ=255)
                   ggTAGTAAATTTGCAAAAGGCGGAAAATACCTAGGTAAAGGTGTTGCTGGTGTAGGATTTGGTATAGGTATGTATGATGACCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTCGCATAATGGTATGAGGCTTGCa                                                                                                               >  2:219463/1‑141 (MQ=255)
                       gtaAATTTGCAAAAGGCGGAAAATACCTAGGTAAAGGTGTTGCTGGTGTAGGATTTGGTATAGGTATGTATGATGACCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTCGCATAATGGTATGACGCTTGCAGCTg                                                                                                           <  1:47427/141‑1 (MQ=255)
                                   aaGGCAGAAAATACCTAGGTAAAGGTGTTGCTGGTGTAGGATTTGGTATAGGTATGTATGATGACCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTTGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGa                                                                                               <  2:263749/141‑1 (MQ=255)
                                          aaaaTACCTAGGTAAAGGTGTTGCTGGTGTAGGATATGGTATAGGTATGTATGATGACCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTTGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGAgagcagc                                                                                        >  2:211036/1‑140 (MQ=255)
                                                ccTAGGTAAAGGTGTTGCTGGTGTAGGATTTGGTATAGGTATGTATGATGACCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTTGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGc                                                                                  <  1:192100/141‑1 (MQ=255)
                                                 cTAGGTAAAGGTGTTGCTGGTGTAGGATTTGGTATAGGTATGTATGATGACCTTGCAAATGATGATAAAACATTTTGAGAGGCGTTGTTGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGCCAGCAGTTGGGGCt                                                                                 >  1:265479/1‑141 (MQ=255)
                                                 cTAGGTAAAGGTGTTGCTGGTGTAGGATTTGGTATAGGTATGTATGATGACCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTTGCATAATGGTATGACGCTTGCGGCTGGATCTGCAGGGACAGCCGTTGGAGCt                                                                                 >  2:174955/1‑141 (MQ=255)
                                                 cTAGGTAAAGGTGTGGCTGGAGTAGGAGATGGTATAGGTATGTATGATGACCTTGCAAATGATGATAAAACATTTGGAGCGGCGATGTTGCATAATAGTATAACGCTTGCAGCTGGATCTGAGGGGGCACCAGTAGGAGCt                                                                                 >  2:234149/1‑141 (MQ=255)
                                                   aGGTAAAGGTGTTGCTGGTGTAGGATTTGGTATAGGTATGTATGATGACCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTTGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTgg                                                                               <  1:106730/141‑1 (MQ=255)
                                                     gTAAAGGTGTTGGTGGTGTAGGATTTGGTATAGGTATGTATGATGACCTTGCAAATGATGATAAAACATTTGGAGAGGCGGTGTTGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGAt                                                                             <  2:92386/141‑1 (MQ=255)
                                                         aGGTGTTGCTGGTGTAGGATTTGGTATAGGTATGTATGATGACCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTTGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAgg                                                                         >  1:150064/1‑140 (MQ=255)
                                                            ggtTGCTGGTGTAGGATTTGGTATAGGTATGTATGATGACCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTTGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAGCGAc                                                                      <  1:230370/140‑1 (MQ=255)
                                                             gtTGCTGGTGTAGGATTTGGTATAGGTATGTATGATGACCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTCGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAGCGACt                                                                     <  1:17647/141‑1 (MQ=255)
                                                             gtTGCTGGTGTAGGATTTGGTATAGGTATGGATGCTGACCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTCGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAGCGACt                                                                     <  2:76339/141‑1 (MQ=255)
                                                              ttGCTGGTGTAGGATTTGGTATAGGTATGTATGATGACCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTTGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAGCGGCtt                                                                    >  1:121897/1‑141 (MQ=255)
                                                              ttGCTGGTGTAGGATTTGGTATAGGTATGTATGATGACCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTCGCATAATGGTATGACGCTTGCAGCTGGCTCTGCAGGGACAGCAGTTGGAGCTGGATTAGCGACtt                                                                    <  1:265336/141‑1 (MQ=255)
                                                                 cTGGTGTAGGATTTGGTATAGGTATGTATGATGACCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTCGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAGCGACTTTTg                                                                 >  1:241354/1‑141 (MQ=255)
                                                                       tAGGATTTGGTATAGGTATGTATGATGACCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTCGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAGCGACTTTTGTTTTAg                                                           >  2:262375/1‑141 (MQ=255)
                                                                             ttGGTATAGGTATGTATGATGACCTTGCAAATGATGATAAAACCTTTGGAGAGGCGTTGTCGCATAATGGTATGACGCTTGCAGCTGGAGCTGCAGGGGAAGCAGTTGGAGCTGGATTAGCGTCTTTTGTTTTAGgtagta                                                     >  1:119062/1‑141 (MQ=255)
                                                                                  ataGGTATGTATGATGACCTTGCAAATGATGATAAAACATTTGGTGAGGCGTTGTTGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATGAGCGACTTTTGTTTTAGGAAGTAATCCa                                                >  1:158489/1‑141 (MQ=255)
                                                                                     ggTATGTATGATGACCTTGCAAATGATGATAAAACATTTGGAGGGGCGTTGTCGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAGCGACTTTTGTTTTAGGAAGTAATCCAGTa                                             >  1:73475/1‑141 (MQ=255)
                                                                                          gtatgATGACCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTTGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAGCGACTTTTGTTTTAGGAAGTAATCCAGTAGGATg                                        >  1:157754/1‑141 (MQ=255)
                                                                                          gtatgATGACCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTTGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAGCAACTTTTGTTTTAGGAAGTAATCCAGTAGGATg                                        >  1:19454/1‑141 (MQ=255)
                                                                                            atgatgACCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTCGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAGCGACTTTTGTTTTAGGAAGTAATCCAGTAGGATggg                                      >  2:19685/1‑141 (MQ=255)
                                                                                               atgaCCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTTGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAGCGACTTTTGTTTTAGGAAGTAATCCAGTAGGATGGGTGa                                   >  2:2104/1‑141 (MQ=255)
                                                                                                           atgatgATAAAACATTTGGGGGGGCGTTGTTGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAGCGACTTTTGTTTTAGGAAGTAATCCAGTAGGATGGGTGATTTTAGCAGGtt                       <  1:236173/141‑1 (MQ=255)
                                                                                                              atgatAAACCATTTGGAGAGGCGTTGTTGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAGCGACTTTTGTTTTAGGAAGTAATCCAGTAGGATGGGTGATTTTAGCAGGTTTgg                    <  1:219613/141‑1 (MQ=255)
                                                                                                              atgatAAAACATTTGGAGAGGCGTTGTTGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAGCGACTTTTGTTTTAGGAAGTAATCCAGTAGGATGGGTGATTTTAGCAGGTTTgg                    <  2:196903/141‑1 (MQ=255)
                                                                                                              atgatAAAACATTTGGAGAGGCGTTGTTGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAGCGACTTTTGTTTTAGGAAGTAATCCAGTAGGATGGGTGATTTTAGCAGGTTTgg                    <  2:81209/141‑1 (MQ=255)
                                                                                                               tgatAAAACATTTGGAGAGGCGTTGTCGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAGCGACTTTTGTTTTAGGAAGTAATCCAGTAGGATGGGTGATTTTAGCAGGTTTGGc                   <  1:262375/141‑1 (MQ=255)
                                                                                                                gatAAAACATTTGGAGAGGCGTTGTCTCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAGCGACTTTTGTTTTAGGAAGTAATCCAGTAGGATGGGTGATTTTAGCAGGTTTGGCt                  <  1:265561/141‑1 (MQ=255)
                                                                                                                      aCATTTGGAGAGGCGTTGTCGCATAATGGTATGACGCTTGCAGCCGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAGCGACTTTTGTTTTAGGAAGTAATCCAGTAGGATGGGTGATTTTAGCAGGTTTGGCTATGAGt            >  2:35396/1‑141 (MQ=255)
                                                                                                                          ttGGAGAGGCGTTGTTGCAGAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAGCGACTTTTGTTTTAGGAAGTAATCCAGTAGGATGGGTGATTTTAGCAGGTTTGGCTATGAGTACAg        <  1:229296/141‑1 (MQ=255)
                                                                                                                          ttGGAGAGGCGTTGTTGCACAATGGTATGACTCCTGCAGCTTGGTCGTCACGGACAACAGTTGGAGCTGGATTACCGACTTTTGTTTTAGGAAGTAATCCACTAGGATCGGTGATTTTAGCAGGTTTGGCTATGAGTACAg        <  2:6823/141‑1 (MQ=255)
                                                                                                                          ttGGAGAGGCGTTGTCGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAGCGACTTTTGTTTTAGGAAGTAATCCAGTAGGATGGGTGATTTTAGCAGGTTTGGCTATGAGTACAg        >  1:22329/1‑141 (MQ=255)
                                                                                                                                agGCGTTTTTGCATAATGGTATGACGCTTGCAGCTGGATCTGCCGGGACAGCAGTTGGAGCTGGATTAGCGACTTTTGTTTTAGGAAGTAAACCAGCAGGATGGGTGATTTTAGCAGGTTTGGCTATGAGTACACTAtttt  <  2:18455/141‑2 (MQ=255)
                                                                                                                                         |                                                                                                                                   
TAATGTGTTTATAGAAAATGGTAGTAAATTTGCAAAAGGCGGAAAATACCTAGGTAAAGGTGTTGCTGGTGTAGGATTTGGTATAGGTATGTATGATGACCTTGCAAATGATGATAAAACATTTGGAGAGGCGTTGTCGCATAATGGTATGACGCTTGCAGCTGGATCTGCAGGGACAGCAGTTGGAGCTGGATTAGCGACTTTTGTTTTAGGAAGTAATCCAGTAGGATGGGTGATTTTAGCAGGTTTGGCTATGAGTACAGTATTTG  >  USA300TCH1516_ALE/654115‑654383

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: ‑