Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	42,835	T→C	28.2%	Q377Q (CAA→CAG)	USA300HOU_0034 ←	IS1272 transposase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	42,835	0	T	C	28.2%	45.2 / 22.9	39	Q377Q (CAA→CAG)	USA300HOU_0034	IS1272 transposase
Reads supporting (aligned to +/- strand):  ref base T (12/16);  new base C (3/8);  total (15/24)
Fisher's exact test for biased strand distribution p-value = 4.77e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.43e-01

GTTCCACATCAATTTTTCTTTGACTGTAGATATTTTTTGTTTCTGGTTCTGAAAGCTTTTTGTTAATTTGGGATTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCATACTTATCATGACGATAGGCATATCTTTTAAAACCTAGCCGTTTATTATTCGGACAAATGAATTCGTCATT  >  CP000730/42696‑42972                                                                                                                                            |                                                                                                                                          gTTCCACATCAATTTTTCTTTGACTGTAGATATTTTTTGTTTCTGGTTCTGAAAGCTTTTTGTTAATTTGGGATTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACAtt                                                                                                                                          >  1:360956/1‑141 (MQ=255)    ccACATCAATTTTTCTTTGACTGTAGATATTTTTTGTTTCTTGTTCTGAAAGCTTTTTGTTAATTTGGGATTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACACTGAt                                                                                                                                       <  1:253017/141‑1 (MQ=255)                       gttGTAGATATTTTTTTGTTCTGGTTCTGAAAGCTTTTTGTTAATTTGGGATTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATATACTGACTTTTCAGAGGACATTCTGa                                                                                                                    <  2:331035/139‑1 (MQ=255)                         tGTAGATATTTTTTGTTTCTGGTTCTGAAAGCTTTTTGTTAATTTGGGATTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCAGAGGACATTCTGAAc                                                                                                                  <  2:169046/141‑1 (MQ=255)                            aGATATTTTTTGTTTCTGGTTCTGAAAGCTTTTTGTTAATTTGGGATTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCAGAGGACTTTCTGAACAat                                                                                                               >  1:126901/1‑141 (MQ=255)                             gATATTTTTTGTTTCTGGTTCTGAAAGCTTTTTGTTAATTTGGGATTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCAGAGGACATTCTGAACAatc                                                                                                              <  2:249422/141‑1 (MQ=255)                               tatTTTTTGTTTCTGGTTCTGAAAGCTTTTTGTTAATTTGGGATTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCAGAGGACATTCTGAACAatcat                                                                                                            >  2:15316/1‑141 (MQ=255)                                atTTTTTGTTTCTGGTTTTGAAAGCTTTTTGTTAATTTGGGATTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTTATACACTGATTTTTCAGAGGACATTCTGAACAatcatc                                                                                                           <  2:362005/141‑1 (MQ=255)                                   ttttGTTTCTGGTTCTGAAAGCTTTTTGTTAATTTGGGATTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCAGAGGACATTCTGAACAATCATcaca                                                                                                        >  1:147672/1‑141 (MQ=255)                                    tttGTTTCTGGTTCTGAAAGCTTTTTGTTAATTTGGGATTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCAGAGGACATTCTGAACAATCATCACAt                                                                                                       <  2:343721/141‑1 (MQ=255)                                       gTTTCTGGTTCTGAAAGCTTTTTGTTAATTTGGGATTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCa                                                                                                    >  2:262236/1‑141 (MQ=255)                                                tCTGAAAGCTTTTTGTTAATTTGGGATTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTg                                                                                           >  1:343137/1‑141 (MQ=255)                                                       gCTTTTTGTTAATTTGGGATTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCACAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGtctc                                                                                    <  2:211471/141‑1 (MQ=255)                                                         tttttCTTAATTTGGGATTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGc                                                                                  <  1:295823/141‑1 (MQ=255)                                                             tGTTAATTTGGGATTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTtat                                                                              >  1:130505/1‑141 (MQ=255)                                                                 taTTTGGGATTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAAcc                                                                          <  2:321912/140‑1 (MQ=255)                                                                 aaTTTGGGATTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAAcc                                                                          <  2:322077/141‑1 (MQ=255)                                                                  aTTTGGGATTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCa                                                                         >  1:126065/1‑141 (MQ=255)                                                                  aTTTGGGATTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCa                                                                         >  1:301039/1‑141 (MQ=255)                                                                  aTTTGGGATTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCa                                                                         >  1:49742/1‑141 (MQ=255)                                                                     tGGGACTTAAAATATTCCCAGTTATAATTCTCCATTAGTTTTTTGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCATAGGACATTCTGAACAATCATCACATTCAAATAATTTCACAGCTCGCTTATAACCATAc                                                                      <  2:182853/141‑1 (MQ=255)                                                                        taTTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACACTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCATACTTa                                                                   <  1:288773/140‑1 (MQ=255)                                                                           tttaaaTATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATATATTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCATACTTATCa                                                                <  2:154549/138‑1 (MQ=255)                                                                                            ataATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACACTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCATACTTATCATGACGATAGGCATATCt                                               <  1:382442/141‑1 (MQ=255)                                                                                               aTTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCATCCTTATCATGACGATAGGCATATCtttt                                            >  1:149805/1‑141 (MQ=255)                                                                                               aTTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCATACTTATCATGACGATAGGCATATCtttt                                            >  1:29604/1‑141 (MQ=255)                                                                                                 tcttcATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATCCTTTGATCTTGCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCATACTTATCATGACGATAGGCATATCTTTTaa                                          <  1:225609/141‑1 (MQ=255)                                                                                                 tcttcATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACTTTGATTATTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCATACTTATCATGACGATAGGCATATCTTTTaa                                          <  1:225613/141‑1 (MQ=255)                                                                                                  cttcATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACACTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTTTCGCTTATAACCATACTTATCATGACGATAGGCATATCTTTTaaa                                         <  1:17333/141‑1 (MQ=255)                                                                                                        tattTTTTTGTTTGTTTTTTTTTTTTTTTTCATACACTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCATACTTATCTTTACGATAGGCATATCTTTTAAAACCTat                                   >  2:393881/1‑140 (MQ=255)                                                                                                           ttttttGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCATACTTATCATGACGATAGGCATATCTTTTAAAACCTAGCCg                                <  2:345938/141‑1 (MQ=255)                                                                                                             ttttGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCATACTTATCATGACGATAGGCATATCTTTTAAAACCTAGCCGtt                              >  1:233361/1‑141 (MQ=255)                                                                                                               ttgtttgtTTTTGAATTGAAGTTCATACATTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCATACTTATCATGACGATAGGCATATCTTTTAAAACCTAGCCGTtta                            <  2:19377/141‑1 (MQ=255)                                                                                                                tgtttgttTTTGAATTGAAGTTCATACACTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCATACTTATCATGACGATAGGCATATCTTTTAAAACCTAGCCGTttat                           <  1:334704/141‑1 (MQ=255)                                                                                                                tgtttgttTTTGAATTGAAGTTCATACACTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCATACTTATCATGACGATAGGCATATCTTTTAAAACCTAGCCGTttat                           <  1:337698/141‑1 (MQ=255)                                                                                                                                     tCATACACTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCATACTTATCATGACGATAGGCATATCTTTTAAAACCTAGCCGTTTATTGTTCAGACAAATAAATTCgc      >  1:50752/1‑140 (MQ=255)                                                                                                                                      cATACATTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCATACTTATCATGACGATAGGCATATCTTTTAAAACCTAGCCGTTTATTGTTCGGACAAATGAATTCGTc     <  1:240748/141‑1 (MQ=255)                                                                                                                                      cATACATTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCATACTTATCATGACGATAGGCATATCTTTTAAAACCTAGCCGTTTATTATTCGGACAAATGAATTCGTc     <  2:50655/141‑1 (MQ=255)                                                                                                                                        tACATTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCCTATAATTTGCAGTCTCGCTTATATCCATACTTAGCATGACGATAGGCATATCTTTTAAAACCTAGCCGTTTATTATTCGGACAAATGAATTCGTCAt   <  1:15316/141‑1 (MQ=255)                                                                                                                                        tACACTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCATACTTATAATGTTAATTCGTAAATCATTTAAAACCTAGCCGTTTATTATTCGGACAAATGAATTCGTCAt   >  1:269687/1‑141 (MQ=255)                                                                                                                                         acacTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCATACTTCTCATGACGATAGGCATATCTTTTAAAACCTAGCCGTTTATTATTCGGACAAATGAATTCGTCAtt  <  2:353836/141‑1 (MQ=255)                                                                                                                                            |                                                                                                                                          GTTCCACATCAATTTTTCTTTGACTGTAGATATTTTTTGTTTCTGGTTCTGAAAGCTTTTTGTTAATTTGGGATTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCATACTTATCATGACGATAGGCATATCTTTTAAAACCTAGCCGTTTATTATTCGGACAAATGAATTCGTCATT  >  CP000730/42696‑42972

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑