BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	2,108,625	C→T	11.3%	G454S (GGC→AGC)	USA300HOU_1971 ←	terminase large subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,108,625	0	C	T	11.3%	88.1 / 2.5	36	G454S (GGC→AGC)	USA300HOU_1971	terminase large subunit
Reads supporting (aligned to +/- strand): ref base C (17/14); new base T (2/2); total (19/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.89e-01

ATTAGTAAACCAACGCATCAAAGGATTGTCTCCATATATTACGTTATGTTTCGCAAACATTGTATCGATACGTGGTGCAAGTAATCCATGTATTGCTTTTGGATTTCTAAGTACTTCAAGTTTTATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGG  >  CP000730/2108497‑2108762

cttaGTAAACCAACGCATCAAAGGATTGTCTCCATATATTACGTTATGTTTCGCAAACATTGTATCGATACGTGGTGCAAGTAATCCATGTATTGCTTTTGGATTTCTAAGTACTTCAAGTTTTATGCCAGCATCCTCaaa                                                                                                                               <  1:200360/140‑1 (MQ=255)

  taGTAAACCAACGCATCAAAGGATTGTCTCCATATATTACGTTATGTTTCGCAAACATTGTATCGATACGTGGTGCAAGTAATCCATGTATTGCTTTTGGATTTCTAAGTACTTCAAGTTTTATGCTAGCATCCTCAAACg                                                                                                                             >  2:191644/1‑141 (MQ=255)

  taGTAAACCAACGCATCAAAGGATTGTCTCCATATATTACGTTATGTTTCGCAAACATTGTATCGATACGTGGTGCAAGTAATCCATGTATTGCTTTTGGATTTCTAAGTACTTCAAGTTTTATGCTAGCATCCTCAAACg                                                                                                                             >  2:194286/1‑141 (MQ=255)

      aaaCCAACGCATCAAAGGATTGTCTCCATATATTACGTTATGTTTCGCAAACATTGTATCGATACGTGGTGCAAGTAATCCATGTATTGCTTTTGGATTTCTAAGTACTTCAAGTTTTATGCCAGCATCCTCAAACGCACg                                                                                                                         >  2:184338/1‑141 (MQ=255)

           aaCGCATCAAAGGATTGTCTCCATATATTACGTTATGTTTCGCAAACATTGTATCGATACGTGGTGCAAGTAATCCATGTATTGCTTTTGGATTTCTAAGTACTTCAAGTTTTATGCCAGCATCATCAAACGCACGTCTTa                                                                                                                    >  2:149879/1‑141 (MQ=255)

            aCGCATCAAAGGATTGTCTCCATATATTACGTTATGTTTCGCAAACATTGTATCGATACGTGGTGCAAGTAATCCATGTATTGCTTTTGGATTTCTAAGTACTTCAAGTTTTATGCCCGCATCCTCAAACGCACGTCTTAc                                                                                                                   >  1:62393/1‑141 (MQ=255)

             cGCATCAAAGGATTGTCTCCATATATTACGTTATGTTTCGCAAACATTGTATCGATACGTGGTGCAAGTAATCCATGTATTGCTTTTGGATTTCTAAGTACTTCAAGTTTTATGCCAGCATCCTCAAACGCACGTCTTACa                                                                                                                  >  2:94521/1‑141 (MQ=255)

                aTCAAAGGATTGTCTCCATATATTACGTTATGTTTCGCAAACATTGTATCGATACGTGGTGCAAGTGATCCATGTATTGCTTTTGGATTTCTAAGTACTTCAAGTTTTATGCCAGCATCCTCAAACGCACGTCTTACAata                                                                                                               <  2:211525/141‑1 (MQ=255)

                           tgttcCATATATGACGTTATGTTTCGCAAACATTGTATCGATACGTGGTGCAAGTAATCCATGTATTGCTTTTGGATTTCTAAGTACTTCAAGTTTTATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCtata                                                                                                    <  2:123801/138‑1 (MQ=255)

                            tctcCATATATTACGTGATGTTTCGCAAACATTGTATCGATACGTGGTGCAAGTAATCCATGTATTGCTTTTGGATTTCTAAGTACTTCAAGTTTTATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATaa                                                                                                   >  1:157774/1‑141 (MQ=255)

                                     atTACGTTATGTTTCGCAAACATTGTATCGATACGTGGTGCAAGTAATCCCTGTATTGCTTTTGGCTTTCTAAGTACTTCAAGTTTTATGCCAGCATCCCCAAACGCACGTCTTACAGTATAAGTTCTGTAATGATAAGca                                                                                          >  1:1943/1‑140 (MQ=255)

                                     atTACGTTATGTTTCGCAAACATTGTATCGATACGTGGTGCAAGTAATCAATGTATTGCTTTTGGATTTCTAAGTACTTCAAGTTTTATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCt                                                                                          >  1:242707/1‑141 (MQ=255)

                                            tATGTTTCGCAGACTTTGTATCGATACGTGGTGCAAGTAATCCATGTATTGCTTTTGGATTTCTAAGTACTTCAAGTTTTATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACtt                                                                                   <  2:27352/141‑1 (MQ=255)

                                                tttCGCAAACATTGTATCGCTACGTGGTGCAAGTAATCCATGTATTGCTTTTGGATTTCTAAGTACTTCAAGTTTTATGCCAGCATCCTCAAACGCACGTCTTACAATCTCAGTTCTATAATTATCAGCTATGACTTTTTc                                                                               >  2:34957/1‑141 (MQ=255)

                                                tttCGCAAACATTGTATCGATACGTGGTGCAAGTAATCCATGTATTGCTTTTGGATTTCTAAGTACTTCAAGTTTTATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTc                                                                               >  2:81640/1‑141 (MQ=255)

                                                   cGCAAACATTGTATCGATACGTGGTGCAAGTAATCCATGTATTGCTTTTGGATTTCTAAGTACTTCAAGTTTTATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTGTATAATTAGCTGCTATGACTTTGTCAAg                                                                            >  1:128903/1‑141 (MQ=255)

                                                       aaCATTGTATCGATACGTGGTGCAAGTAATCCATGTATTGCTTTTGGATTTCTAAGTACTTCAAGTTTTATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCa                                                                        >  1:9/1‑141 (MQ=255)

                                                           ttGTATCGATACGTGGTGCAAGTAATCCATGTATTGCTTTTGGATTTCTAAGTACTTCAAGTTTTATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATAtt                                                                    <  2:160989/141‑1 (MQ=255)

                                                            tGTATCGATACGTGGTGCAAGTAATCCATGTATTGCTTTTGGATTTCTAAGTACTTCAAGTTTTATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATAttt                                                                   <  1:216036/141‑1 (MQ=255)

                                                                       gtggtgCAAGTAATCCATGTATTGCTGTTGGATTTCTAAGTACTTCAAGTTTTATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCt                                                        <  1:265735/141‑1 (MQ=255)

                                                                              aaGTAATCCATGTATTGCTTTTGGATTTCTAAGTACTTCAAGTTTTATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTaaaaa                                                 <  2:207470/141‑1 (MQ=255)

                                                                               aGTAATCCATGTATTGCTTTTGGATTTCTAAGTACTTCAAGTTTTATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTCGCCTTTAAAAAc                                                >  1:179243/1‑141 (MQ=255)

                                                                                      cATGTATTGCTTTTGGATTTCTAAGTACTTCAAGTTTTATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCaa                                         <  2:157774/141‑1 (MQ=255)

                                                                                           ttttcTTTTGGATTTCTAAGTACTTCAAGTTTTATGCCAGCAGCCTCAACCGCACGTCTTACAATATCAGTTCTATAATCATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACtata                                    <  2:203530/137‑1 (MQ=255)

                                                                                              tcTTGTGGATTTGTATGTACTTGTAGTTTTATGCAAACAGCCTGCAGCAGATGTTTTACAATATCGGGTTTATAATTCTCAGCTCTGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTACAAACCAATCACCTatatat                                 <  2:99754/140‑1 (MQ=255)

                                                                                              gCTTTTGGATTTCTAAGTACTTCAAGTTTTATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTatatat                                 >  2:65587/1‑141 (MQ=255)

                                                                                               cTTTTGGATTTCTAAGTACTTCAAGTTTTATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCCATCAACTATATAtt                                >  1:46528/1‑141 (MQ=255)

                                                                                                   tGGATTTCTAAGTACTTCAAGTTTTATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATAttcaat                            <  2:207553/141‑1 (MQ=255)

                                                                                                         tCTAAGTACTTCAAGTTTTATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATAttcaatttcaat                      >  2:67821/1‑141 (MQ=255)

                                                                                                           tAAGTACTTCAAGTTTTATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGa                    <  1:162574/141‑1 (MQ=255)

                                                                                                             aGTACTTCAAGTTTTATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATAATCATCTCTTGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGAca                  <  1:149879/141‑1 (MQ=255)

                                                                                                               tACTTCAAGTTTTATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGAcatc                >  1:7650/1‑141 (MQ=255)

                                                                                                                      aGTTTTATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCg         <  1:94521/141‑1 (MQ=255)

                                                                                                                        ttttATGCTAGCCTCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGAc       <  1:194286/141‑1 (MQ=255)

                                                                                                                        ttttATGCTAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGAc       <  1:191644/141‑1 (MQ=255)

                                                                                                                             tGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATgg  >  1:36833/1‑141 (MQ=255)

ATTAGTAAACCAACGCATCAAAGGATTGTCTCCATATATTACGTTATGTTTCGCAAACATTGTATCGATACGTGGTGCAAGTAATCCATGTATTGCTTTTGGATTTCTAAGTACTTCAAGTTTTATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGG  >  CP000730/2108497‑2108762

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: `‑`