Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	602,466	G→T	8.2%	intergenic (+56/‑104)	hchA → / → araB	Molecular chaperone Hsp31 and glyoxalase 3/Ribulokinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	602,466	0	G	T	8.2%	234.7 / 2.4	89	intergenic (+56/‑104)	hchA/araB	Molecular chaperone Hsp31 and glyoxalase 3/Ribulokinase
Reads supporting (aligned to +/- strand):  ref base G (31/48);  new base T (6/2);  total (38/51)
Fisher's exact test for biased strand distribution p-value = 6.74e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACAGGTGACAGTCCTTTAGCTTCAAATGAGTTAGGAAAATTAGCAGTTAATGAAATGTTAAATGCAATACAAAATAAATAATTAAA‑TATTAATT‑AGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATGGAGGAAACATGATGTCTTATAGCATTGGAATTGATTATGGAACTGCTT  >  USA300TCH1516_ALE/602330‑602606                                                                                                                                            |                                                                                                                                             aCAGGTGACAGTCCTTTAGCTTCAAATGAGTTAGGAAAATTAGCAGTTAATGAAATGTTAAATGCAATACAAAATAAATAATTAAA‑TATTAATT‑AGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCaa                                                                                                                                          >  2:52966/1‑141 (MQ=255) aCAGGTGACAGTCCTTTAGCTTCAAATGAGTTAGGAAAATTAGCAGTTAATGAAATGTTAAATGCAATACAAAATAAATAATTAAA‑TATTAATT‑AGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCaa                                                                                                                                          <  1:960300/141‑1 (MQ=255) aCAGGATACAGTCCTTTAGCTTCAAATGAGTTAGGAAAATTAGCTGTTAATGAAATGTTAAATGCAATACAAAATAAATAATTAAA‑TATTAATT‑AGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGTCaa                                                                                                                                          <  2:545035/141‑1 (MQ=255)  cAGGTGACAGTCCTTTAGCTTCAAATGAGTTAGGAAAATTAGCAGTTAATGAAATGTTAAATGCAATACAAAATAAATAATTAAA‑TATTAATT‑AGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGTCaaa                                                                                                                                         >  2:434136/1‑141 (MQ=255)  cAGGTGACAGTCCTTTAGCTTCAAATGAGTTAGGAAAATTAGCAGTTAATGAAATGTTAAATGCAATACAAAATAAATAATTAAA‑TATTAATT‑AGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑‑TTTTTTTTGGCaaaa                                                                                                                                        >  2:17012/1‑141 (MQ=255)      tGACAGTCCTTTAGCTTCAAATGAGTTAGGAAAATTAGCAGTTAATGAAATGTTAAATGCAATACAAAATAAATAATTAAA‑TATTAATT‑AGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAAttt                                                                                                                                     <  2:627163/141‑1 (MQ=255)        aCAGTCCTTTAGCTTCAAATGAGTTAGGAAAATTAGCAGTTAATGAAATGTTAAATGCAATACAAAATAAATAATTAAA‑TATTAATT‑AGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑‑TTTTTTTTGGCAAAATCTAAg                                                                                                                                  <  1:722252/141‑1 (MQ=255)         cAGTCCTTTAGCTTCAAATGAGTTAGGAAAATTAGCAGTTAATGAAATGTTAAATGCAATACAAAATAAATAATTAAA‑TATTAATT‑AGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAg                                                                                                                                  >  2:139078/1‑141 (MQ=255)             ccTTTAGCTTAAAATGAGTTAGGAAAATTAACAATTAATGAAATGTTAAATGAAATACAAAATAAATAATTAAA‑TATTAATT‑AGAGGAGCCTCATATGTAAATTTATGAGGTCTC‑TTTTTTTTTGGCAAAATTTAAGTGAt                                                                                                                              <  2:76347/141‑1 (MQ=255)             actatAGCTTAAAAAGAGTTAGGAAAATTAGCAGTTAATGAAATGTTAAATGCAATACAAAATAAATAATTAAA‑TATTAATT‑AGATGACCCGCAAATGTAAACGTATTATGGCTC‑TTTTTTTTTGGCAAAATTTAAGGGAt                                                                                                                              <  2:798415/137‑1 (MQ=255)                 tAGCTTCAAATGAGGTAGGAAAATTAGCCGTTAATGAAATGTTAAATGCAATACAAAATAAATAATTAAA‑TATTAATT‑AGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACtt                                                                                                                          <  2:934789/141‑1 (MQ=255)                  atcTTCAAATGATTTAGAAAAATTAGCTGTTAATGAAATGTTAAAAGCAATACAAAATAAATAATTAAA‑TATTAATT‑AGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGTCAAAATTTAAGTGATACTTg                                                                                                                         <  2:981465/139‑1 (MQ=255)                  aGCTTCAAATGAGCTAGGAAAATTAGCAGTTAATGAAATGTTAAATGCAATACAAAATAAATAATTAAA‑TATTAATT‑AGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTg                                                                                                                         <  2:763358/141‑1 (MQ=255)                   gCTTAAAATGAGTTAGGAAAATTAGCAGTTAATGAATTGTTAAATGCAATACAAAATAAATAATTAAA‑TATTAATT‑AGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGt                                                                                                                        <  1:696234/141‑1 (MQ=255)                   gCTTAAAATGAGTTAGGAAAATTAGCAGTTAATGAAATGTTAAATGCAATACAAAATAAATAATTAAA‑TATTAATT‑AGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGt                                                                                                                        <  2:63222/141‑1 (MQ=255)                      tCAAATGAGTTAGGAAAATTAGCAGTTAATGAAATGTTAAATGCAATACAAAATAAATAATTAAA‑TATTAATT‑AGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTaaa                                                                                                                     <  1:782705/141‑1 (MQ=255)                      tCAAATGAGTTAGGAAAATTAGCAGTTAATGAAATGTTAAATGCAATACAAAATAAATAATTAAA‑TATTAATT‑AGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTaaa                                                                                                                     <  2:921067/141‑1 (MQ=255)                      acAAATGAGTTAGGAAAATTAGAGGTTAATTAAATGTCAAACGCAATACAAAATAAATAATAAAA‑TATTAATT‑AGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTaaa                                                                                                                     <  1:576521/140‑1 (MQ=255)                        aaaTGAGTTAGGAAAATTAGCAGTTAATGAAATGTTAAATGCAATACAAAATAAATAAGTAAA‑TATTAATT‑AGAGGAGCCTCATATGTAAAAGTATGAGTGCAA‑TTTTTTTTTGGGAAAATTTGAGTGATACTTGTaacaa                                                                                                                   >  2:886736/1‑138 (MQ=255)                           tGAGTTAAGTAAATTATCAGTTAATGAAATGTTAAATGCAAAAAAAAATAAATAATTAAA‑TATTAATT‑AGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTTGCAAAATTTAAGTGATACTTGTAAAATAGa                                                                                                                <  2:834124/141‑1 (MQ=255)                             aGTAAGGAAAATTAGCAGTTAATGAAATGTTAAATGCAATACAAAATAAACAATTAAA‑TATTACTT‑AGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATATTTGTAAAATAGAAc                                                                                                              <  2:725457/141‑1 (MQ=255)                              gTTAGGAAAATTAGCAGTTAATGAAATGTTAAATGCAATACAAAATAAATAATTAAA‑TATTAATT‑AGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCACAAATTAAGTGATACTTGTAAAATAGaaac                                                                                                             >  1:648168/1‑139 (MQ=255)                              gTTAGGAAAATTAGCAGTTAATGAAATGTTAAATGCAATACAAAATAAATAATTAAA‑TATTAATT‑AGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAAcc                                                                                                             >  1:834551/1‑141 (MQ=255)                              gTTAGGAAAATTAGCAGTTAATGAAATGTTAAATGCAATACAAAATAAATAATTAAA‑TATTAATT‑AGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAAcc                                                                                                             >  1:696183/1‑141 (MQ=255)                              gTTAGGAAAATTAGCAGTTAATGAAATGTTAAATGCAATACAAAATAAATAATTAAA‑TATCAATT‑AGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAAcc                                                                                                             >  1:146259/1‑141 (MQ=255)                                 aGGAAAATTAGCAGTTAATGAAATGTTAAATGCAATACAAAATAAATAATTAAA‑TATTAATT‑AGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGTAAAATTTAAGTGATACTTGTAAAATAGAACCtct                                                                                                          >  2:734019/1‑139 (MQ=255)                                   gAAAATTAGCGGTTAATGAAATGTCAAATGCAATACAAAATCAATCATAAACGTTTTAATT‑TGGGAGGCATTAGA‑GAAAATGTATGCGGCCTC‑TTTTTTTTTGGCAAATTTGGAGTGATGCTTGTAAAATAGAACCtatta                                                                                                        >  1:775912/1‑141 (MQ=255)                                   gAAAATTAGCAGTTAATGAAATGTTAAATGCAATACAAAATAAATAATTAAA‑TATTAATT‑AGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCtatta                                                                                                        >  1:694492/1‑141 (MQ=255)                                    aaaaTTAGCAGTTAATGAAATGTTAAATGCAATACAAAATAAATAATTAAA‑TATTAATT‑AGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCtattat                                                                                                       <  2:1021505/141‑1 (MQ=255)                                      aaTGAGCAGTTAATGAAATGTTAAATGCAATACAAAATAAATAATTAAA‑TATTAATT‑AGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGa                                                                                                     <  2:474891/141‑1 (MQ=255)                                        ttAGCAGTTAATGAAATGTTAAATGCAATACAAAATAAATAATTAAA‑TATTAATT‑AGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGt                                                                                                   >  2:978468/1‑141 (MQ=255)                                         aaGCAGATAATGAAACATTAAACACACAACAAAACAAATAATTAAA‑TATAAATT‑AGAGGAACCTAATATGTAAATGAATGAGAGCTC‑TCTTTTTTTCGCAAAATTTAAGTGATACTTGTATAATAGAACCTATTATGAGTa                                                                                                  <  1:645050/140‑1 (MQ=255)                                          agtaGTTAATGAAATGTTAAATGCAATACAAAATAAATAATTAAA‑TATTAATT‑AGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCATAGTTTAACTGATACTTGTAAAATAGAACCTATTATGACTAt                                                                                                 >  2:145290/4‑141 (MQ=255)                                          aGCAGTTAATGAAATGTTAAATGCAATACAAAATAAATAATTAAA‑TACTAATT‑AGAGGAGCCTCATATGTACATGTCTGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTACAATAGCACCTATTATAGGTAt                                                                                                 >  1:1011428/1‑141 (MQ=255)                                            cAGTTAATGAAATGTTAAATGCAATACAAAATAAATAATTAAA‑TATTAATT‑AGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGa                                                                                               >  2:938517/1‑141 (MQ=255)                                            cAGTTAATGAAATGTTAAATGCAATACAAAATAAATAATTAAA‑TATTAATT‑AGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGa                                                                                               >  1:938967/1‑141 (MQ=255)                                              ataaagaaaaTATAAAAAGCAAAAAAAAATAAAAAATTAAA‑TATTAATT‑AGAGGAGACTAATATGTAAATGTATGAGGGCTCTTTTTTTTTTTGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGAt                                                                                              <  2:860734/134‑1 (MQ=255)                                                taagaaaaTGTTAAATGCAATACAAAATAAATAATTAAA‑TATTATTT‑AAAGGATTCTCAAATGTAAATTTATGAGGGTTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTa                                                                                           <  2:690707/136‑1 (MQ=255)                                                          ttAAATGCAATTAAAAATAAATAATTAAA‑TATTAATT‑AGAGGAGACTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCt                                                                                 <  1:742245/141‑1 (MQ=255)                                                          ttAAATGCAATACAAAATAAATAATTAAA‑TATGAATT‑AGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCt                                                                                 <  2:54414/141‑1 (MQ=255)                                                          ttAAATGAAAAACAAAATAAATAATTAAT‑CATTAATTAACCGGGGGATCGTGTG‑AAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCt                                                                                 <  1:1037398/141‑1 (MQ=255)                                                             aaTGCAATACAAAATAAATAATTAAA‑GATTAATT‑AGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGc                                                                              <  2:264744/141‑1 (MQ=255)                                                                   aTACAAAATAAATAATTAAA‑TATTAATT‑AGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACt                                                                        <  2:499336/141‑1 (MQ=255)                                                                    aaaaaaaaaaaaaATTAAA‑AATTAATT‑AAAGGAGCCTCATATGTAAATGTATGAGAGCTC‑GTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACta                                                                       <  2:526625/138‑1 (MQ=255)                                                                         aataaataATTAAA‑TATTAATT‑AGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAAc                                                                  >  1:849119/1‑141 (MQ=255)                                                                           taaataaTTAAA‑TATTAATA‑AGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTATTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTACGATTTAAGAAAACGCTTGCATAACTAATAAcac                                                                >  2:593747/1‑139 (MQ=255)                                                                            aaataaatAAA‑AATTAATT‑AGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACCCTTGCAAAACTAATAACCGc                                                               <  1:643457/141‑1 (MQ=255)                                                                            aaataaTTAAA‑TATTAATT‑AGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTTGCAAATTTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAACACGCTTCCAAAACTAATAACCGc                                                               >  2:40105/1‑141 (MQ=255)                                                                            aaataaTTAAA‑TAATAATT‑AGAGGACCCTCATATGTAAATGTATGAGGGCTA‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGc                                                               <  2:590986/141‑1 (MQ=255)                                                                                  aaaaa‑aATTAATT‑AGAGGAGACTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAg                                                         <  1:1063230/139‑1 (MQ=255)                                                                                   aaaa‑aATAAATA‑AAAGGAGCCTAAAATGTAAAGGTATGAGGGCTT‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGc                                                        <  1:1059292/140‑1 (MQ=255)                                                                                          ataatt‑aGAGGGGCGTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATg                                                  <  2:123415/140‑1 (MQ=255)                                                                                          ataatt‑aGAGGAGCCTCATATGTAAATGTATGAGGGCTT‑TTTTTTTTTGGCAAAATTGAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATg                                                  <  1:512192/140‑1 (MQ=255)                                                                                            aatt‑aGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTACTATTTTTTTAGTGCTGTATGTAAAATAGACCCTTTTTTTACTATGTTTAATGAATACGCTTTCAAAACTAATAACCCCAACTAGATATGTgga                                                >  2:820553/1‑141 (MQ=255)                                                                                              tt‑aGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGTCAAAATTTAAGTGATACATGTAAAATAGAACCTATTATGAATATAATTTAAGAAAACGCCTCCAGAACTCATAACCGCAACTAACGATATgtaag                                              >  2:874642/1‑137 (MQ=255)                                                                                                   gggagCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATGGAGGAAAc                                          <  2:379679/140‑1 (MQ=255)                                                                                                   aggagCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTTTTTTTTTTTATATAATACGTGTAAAATAGAACCTATTATGAGGATGATTTATGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGGTATGGAGGaaaa                                          >  2:752803/1‑140 (MQ=255)                                                                                                   aggagCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACGGCAACTAGCGATATGGGGGaaaa                                          >  1:27970/1‑140 (MQ=255)                                                                                                   aggagCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATGGAGGAAAc                                          >  1:348481/1‑141 (MQ=255)                                                                                                    ggagCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTAAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATGGAGGAAACa                                         >  1:411646/1‑141 (MQ=255)                                                                                                    ggagCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTAAAGTCTAAATTTACGTGTTTCGTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATGGAGGAAACa                                         >  1:509840/1‑141 (MQ=255)                                                                                                    ggagCCAAATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATGGAGGAAACa                                         <  2:11660/141‑1 (MQ=255)                                                                                                    ggagCCAAATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATGGAGGAAACa                                         <  1:621774/141‑1 (MQ=255)                                                                                                      agCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTTTTTTTTTTTAGGTGATACTTGTAAAATAAAACCTATTATGTGAATGGTTTAAGAAAACGCTTCCACACCTAATAACCGCAACTAGCGCTCTAGGAGAAACatg                                       >  2:397221/1‑141 (MQ=255)                                                                                                      agCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATAAGGAGGAAACatg                                       >  1:297636/1‑141 (MQ=255)                                                                                                         ctaatatGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATGGAGGAAACatgatg                                    <  2:807546/138‑1 (MQ=255)                                                                                                            atatGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATGGAGGAAACATGATGTCt                                 <  2:938967/141‑1 (MQ=255)                                                                                                            atatGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGGGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATGGAGGAAACATGATGTCt                                 <  2:397744/141‑1 (MQ=255)                                                                                                             tatGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCTAAATTTAAGTGATACGTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTACAAAACTAATAACCGCAACTAGCGATATGGAGGAAACATGATGTCtt                                <  1:719459/141‑1 (MQ=255)                                                                                                               tGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATGGAGTAAACATGATGTCTtat                              <  2:383292/141‑1 (MQ=255)                                                                                                                gTAAATGTAGGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATGGAGGAAACATGATGTCTtata                             <  1:229840/141‑1 (MQ=255)                                                                                                                 tAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAACCTAATAACCGCAACTAGCGATATGGAGGAAACATGATGTCTTTTAg                            >  2:56668/1‑141 (MQ=255)                                                                                                                   aaTTTATAAGGGCTT‑TTTTTTTTTGGCAAAATTTAAGTGATACGTGTAAAATAGAAACTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATGGAGGAAACATGATGTCTTATAGCa                          <  1:689564/141‑1 (MQ=255)                                                                                                                   aaTGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATGGAGGAAACATGATGTCTTATAGCa                          >  1:591915/1‑141 (MQ=255)                                                                                                                   aaTGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATGGAGGAAACATGATGTCTTATAGCa                          <  1:689722/141‑1 (MQ=255)                                                                                                                    aTGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATGGAGGAAACATGATGTCTTATAGCAt                         <  1:938517/141‑1 (MQ=255)                                                                                                                    aTGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATGGAGGAAACATGATGTCTTAAAGCAt                         >  1:611483/1‑141 (MQ=255)                                                                                                                        aTGAGGGCTC‑TTTTTTTTTTGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATGGAGGAAACATGATGTCTTATAGCATTCGa                     >  2:248289/1‑141 (MQ=255)                                                                                                                        aTGAGGGCAC‑ATTTTTTTAGGCAAAAATTAAGTGATACTTGTAAAAAAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATGGAGGAAACATGATGTCTTATAGCATTGGa                     <  1:17944/141‑1 (MQ=255)                                                                                                                         tGAGGGATA‑TTTTTTTTTGGAAAACTTTAGGTCAAGCATGAAAAATATAACCAAAAATAGCTAACATAGAAAAAAACGCTTCGAAAACAAATAACCGCAACTAACGAGATGGAGGAAACATGATGTCTTATAGCATTGGaa                    <  2:883107/141‑1 (MQ=255)                                                                                                                          gagaGCAC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATGGAGGAAACATGATGTCTTATAGCATTGGAAt                   <  1:360275/141‑1 (MQ=255)                                                                                                                          aaGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATGGAGGAAACATGATGTCTTATAGCATTGGAAt                   <  1:360323/140‑1 (MQ=255)                                                                                                                              gCTC‑TTTTTTTTTTTTTAAATTTAAGTGATACTTGTAAAATATAACCTTTTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTATCGATATGGAGGGAACATGATGTCTTATAGCATTggtagttat               >  2:956491/1‑134 (MQ=255)                                                                                                                               ctc‑tTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGGTTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGCTATGGAGGAAACATGATGTCTTATAGCATAGGAATTGAtt              >  1:45047/1‑141 (MQ=255)                                                                                                                                tc‑tTTTTTTTTTTCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATGGAGGAAACATGATGTCTTATAGCATTGGAATTGATTa             >  2:75393/1‑141 (MQ=255)                                                                                                                                   tttttttttGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATGGAGGAAACATGATGTCTTATAGCATTGGAATTGATTATg           <  2:849345/141‑1 (MQ=255)                                                                                                                                    ttttttttGGCAGAATTTAAGTGATACTTGTAAAATAGAACCTATTATGGGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATCGAGGAAACATGATGTCTTATAGCATTGGAATTGATTATgg          >  1:750705/1‑141 (MQ=255)                                                                                                                                    ttttttttGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATGGAGGAAACATGATGTCTTATAGCATTGGAATTGATTATgg          >  1:312424/1‑141 (MQ=255)                                                                                                                                     tttttatGACAAAAATTAAGTGAAAATTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAAATAATAACCGCAACTAGTGATATGGAGGAAACATGATGTCTTACAGCACTGGAATTGATTATGGa         <  1:544683/141‑1 (MQ=255)                                                                                                                                            ggCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATGGAGGAAACATGATGTCTTATAGCATTGGAATTGATTATGGAACTGCtt  >  1:224115/1‑141 (MQ=255)                                                                                                                                            |                                                                                                                                             ACAGGTGACAGTCCTTTAGCTTCAAATGAGTTAGGAAAATTAGCAGTTAATGAAATGTTAAATGCAATACAAAATAAATAATTAAA‑TATTAATT‑AGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATGGAGGAAACATGATGTCTTATAGCATTGGAATTGATTATGGAACTGCTT  >  USA300TCH1516_ALE/602330‑602606

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑