Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	2,108,728	A→G	9.8%	Y419Y (TAT→TAC)	USA300HOU_1971 ←	terminase large subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,108,728	0	A	G	9.8%	100.7 / 3.7	41	Y419Y (TAT→TAC)	USA300HOU_1971	terminase large subunit
Reads supporting (aligned to +/- strand):  ref base A (14/23);  new base G (2/2);  total (16/25)
Fisher's exact test for biased strand distribution p-value = 6.37e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.52e-01

TTGCTTTTGGATTTCTAAGTACTTCAAGTTTTATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTTTTTCCCATTCTTTAATAGGAGGTTCTAATTTGACATCATCCAAAAACCCTTGTCTTACAAACGAATGTCCTAACCAAATGTAATCATCGTT  >  CP000730/2108589‑2108868                                                                                                                                            |                                                                                                                                             ttGCTTTTGGATTTCTAAGTACTTCAAGTTTTATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACtatat                                                                                                                                             <  1:84378/141‑1 (MQ=255)          gATTTCTAAGTACTTCAAGTTTTATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATAttcaattt                                                                                                                                    >  1:4218/1‑141 (MQ=255)              tCTAAGTACTTCAAGTTTTATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATAttcaatttcaat                                                                                                                                >  1:536832/1‑141 (MQ=255)                  aGTACTTCAAGTTTTATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGAca                                                                                                                            <  2:98191/141‑1 (MQ=255)                          aaGTTTTATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACatcatcatc                                                                                                                    >  1:209909/1‑141 (MQ=255)                            gTTTTATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGa                                                                                                                  <  1:620362/141‑1 (MQ=255)                            gTTTTATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTAAAAAAAAAAAAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGa                                                                                                                  <  2:279998/141‑1 (MQ=255)                             ttttATGCCAGCATCCGCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGaa                                                                                                                 >  2:660376/1‑140 (MQ=255)                              tttATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACa                                                                                                                <  1:20587/141‑1 (MQ=255)                                tATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATGTATTCAATTTCAATTACATCATCATCGACAAt                                                                                                              >  1:152216/1‑141 (MQ=255)                                tATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATGTATTCAATTTCAATGACATCATCATCGACAAt                                                                                                              >  1:181118/1‑141 (MQ=255)                                      aGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTaaa                                                                                                        >  2:247590/1‑141 (MQ=255)                                           ccTCAAACGCACGTTTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATc                                                                                                   <  1:264370/141‑1 (MQ=255)                                           ccTCAAACGCACGTCTTACAATATCATTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATc                                                                                                   <  1:618481/141‑1 (MQ=255)                                              cAAACGCACGTCTTACAATTTCAGTTCTATATTTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCa                                                                                                <  1:217066/141‑1 (MQ=255)                                              cAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCa                                                                                                <  1:66899/141‑1 (MQ=255)                                                            aCAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTTTTTCCCATTCt                                                                                  >  2:587389/1‑141 (MQ=255)                                                             cAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTTTTTCCCATTCtt                                                                                 <  1:492451/141‑1 (MQ=255)                                                                  tCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTGTTTCCCATTCTTTAATa                                                                            <  1:171186/141‑1 (MQ=255)                                                                  tCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTATAGTGATTTTTTACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTTTTTCCCATTCTTTAATa                                                                            <  1:454024/141‑1 (MQ=255)                                                                     gTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTTTTTCCCATTCTTTAATagga                                                                         <  2:112309/141‑1 (MQ=255)                                                                         tataATTATCAGCTATGACTTTTTCAAGCCCATATTTTGCTCTAGCCTTTAAAAACCAATTAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTTTTTCCCATTCTTTAATAGGAGGtt                                                                     <  1:324789/141‑1 (MQ=255)                                                                               tATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTTTTTCCCATTCTTTAATAGGAGGTTCTAAtt                                                               <  1:566703/141‑1 (MQ=255)                                                                                  cAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCTCATTTTTTCCTATTTTTTATTAGAAGGTTATCATTTgt                                                            >  2:411737/1‑140 (MQ=255)                                                                                  cAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTTTTTCCCATTCTTTAATAGGAGGTTATACtttat                                                            >  2:164553/1‑139 (MQ=255)                                                                                   aGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGTCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTTTTTACCATTCTTTAATAGGTGGTTCTTATTTGAc                                                           >  2:546059/1‑141 (MQ=255)                                                                                     cTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCCTCATCGACAATGGTCAATAACCCCATTTTTTCCCTTTCTTTCATAGTAGGTTCTACATTTAcat                                                         >  2:194927/1‑141 (MQ=255)                                                                                       aTGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTTTTTCCCATTCTTTAATAGGAGGTTCTAATTTGAcatca                                                       <  2:536832/141‑1 (MQ=255)                                                                                        tGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTTTTTCCCATTCTTTAATAGGAGGTTCTAATTTGAcatcat                                                      <  2:463258/141‑1 (MQ=255)                                                                                          aCTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTTTTTCCCATTCTTTAATAGGAGGTTCTAATTTGACATCATcc                                                    <  2:209909/141‑1 (MQ=255)                                                                                                 cAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCATTGACATCATCATCGACACTGGTCAATAATCCCATTTTTTCCCAATCTTTAATGGGAGGTCTAAAGTTGACATCATCCACAAAcc                                             <  1:490659/141‑1 (MQ=255)                                                                                                     cccATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTTTTTCCCATTCTTTAATAGGAGGTTCTAATTTGACATCATCCAAAAACCCTTg                                         >  1:76055/1‑141 (MQ=255)                                                                                                        atatTTTTCCCTAGCCTTTATAACCCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTTTTTCCCATTCTTTAATAGGAGGTTCTAATTTGCCATCATCCAAAAACCCTTGTCt                                      <  1:390478/141‑1 (MQ=255)                                                                                                           tttttCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTTTTTCCCATTCTTTAATAGGAGGTTCTAATTTGACATCATCCAAAAACCCTTGTCTTAc                                   >  1:381389/1‑141 (MQ=255)                                                                                                             tttCTCTAGCCTTTAAAAACCAATCAACTATGTATTCAATTTCAATGACTTCATCATCGACAATGGTCAATAATCCCATTTTTTCCCATTCTTTAATAGGAGGTTCTAATTTGACATCATCCAAAAACCCTTGTCTTACaa                                 <  2:152216/141‑1 (MQ=255)                                                                                                             tttCTCTAGCCTTTAAAAACCAATCAACTATGTATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTTTTTCCCATTCTTTAATAGGAGGTTCTAATTTGACATCATCCAAAAACCCTTGTCTTACaa                                 <  2:181118/141‑1 (MQ=255)                                                                                                             tgtctcTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGATAATGGTCAATAATCCCATTTTTTCCCCTTCTTTAATAGGAGGTTCTAATTTGACATCATCCAAAAACCCTTGTCTTACaa                                 <  2:7737/139‑1 (MQ=255)                                                                                                                  ctAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTTTTTCCCATTCTTTAATAGGAGGTTCTAATTTGACATCATCCAAAAACCCTTGTCTTACAAACGaa                            <  2:208603/141‑1 (MQ=255)                                                                                                                     gCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTTTTTCTTTTTTTTTAATACGAGGTTCTTATTTGGAGTGTTCCAAAGACACTTTTCTTACAAACGaagtt                         >  2:201727/1‑138 (MQ=255)                                                                                                                         ttAAAAACCATTGAACTATATAGTCAATTTCAATGACATCCTCATCGACAATTGTCGATAATCCCATTTTTTCCCATTCTTTAATAGGATGTTCTAATTTGACATCATCCAAAAACCCTTGTCTTACAAACGAATGTCCTa                     <  2:125816/141‑1 (MQ=255)                                                                                                                         ttAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTTTTTCCCATTCTTTAATAGGAGGTTCTAATTTGACATCATCCAAAAACCCTTGTCTTACAAACGAATGTCCTa                     >  2:422908/1‑141 (MQ=255)                                                                                                                                    tccaCTATATATACAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTTTTTCCCATTCTTTAATAGGAGGTTCTAATTTGACATCATCCAAAAACCCTTGTCTTACAAACGAATGTCCTAACCAAATGTaa          <  2:373950/138‑1 (MQ=255)                                                                                                                                            atatTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTTTTTCCTATTTTTTAATAGGAGGTTCTAATTTGACATCATCCAAAAACCCTTGTCTTACAAACGAATGTCCTAACCAAATGTAATCATCGtt  >  2:529545/1‑141 (MQ=255)                                                                                                                                            |                                                                                                                                             TTGCTTTTGGATTTCTAAGTACTTCAAGTTTTATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTTTTTCCCATTCTTTAATAGGAGGTTCTAATTTGACATCATCCAAAAACCCTTGTCTTACAAACGAATGTCCTAACCAAATGTAATCATCGTT  >  CP000730/2108589‑2108868

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: ‑