Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,236,856	A→T	L303I (TTA→ATA)	rho ←	Transcription termination factor Rho

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,236,856	0	A	T	100.0%	50.7 / NA	20	L303I (TTA→ATA)	rho	Transcription termination factor Rho
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (8/12);  total (8/12)

TCCTTTAAATTCTTCGTAAATCATATCGTCCATACGTGAACCCGTATCAACTAATGCAGTTGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTAAAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGAATAACTAAGTTATAAGCGCGTGCTAATCTCGTTATAGAATCCATTAAAATAATGACATCTTCCCCAATTTCTACTAAACGCTTTG  >  USA300TCH1516_ALE/2236725‑2236987                                                                                                                                    |                                                                                                                                    tCCTTTAAATTCTTCGTAAATCATATCGTCCATACGTGAACCCGTATCAACTAATGCAGTTGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAgg                                                                                                                            >  1:391710/1‑141 (MQ=255)        aaTTCTTCGGAAATCATATCGTCCATACGTGAACCCGTATCAACTAATGCAGTTGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTaaa                                                                                                                     <  1:464520/141‑1 (MQ=255)           tcttcCTAAATCATATCGTCCATACGTGAACCCGTATCAACTAATGCAGTTGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTAAacca                                                                                                                  <  1:396432/141‑1 (MQ=255)                               cATCCGTGAACCCGTATCAACTAATGCAGTTGCAAGTATCGTTAAACTTCCACCCGCCTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACt                                                                                              <  1:332911/141‑1 (MQ=255)                                   cGTGAACCCGTATCAACTAATGCAGTTGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTtggt                                                                                          >  1:385514/1‑141 (MQ=255)                                        aCCCGTATCAACTAATGCAGTTGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGAAt                                                                                     <  1:167798/141‑1 (MQ=255)                                        aCCCGTATCAACTAATGCAGTTGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGAAt                                                                                     <  1:183996/141‑1 (MQ=255)                                            gTATCAACTAATGCAGTTGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGGATAACt                                                                                 >  1:2159/1‑141 (MQ=255)                                                    tAATGCAGTTGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGAATAACTAAGTtata                                                                         <  1:68227/141‑1 (MQ=255)                                                            ttGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGAATAACTAAGTTATAAGCGCGTg                                                                 <  1:476895/141‑1 (MQ=255)                                                            ttGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGAATAACTAAGTTATAAGCGCGTg                                                                 <  1:245604/141‑1 (MQ=255)                                                               cAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGAGTATAGATGCAGGATCTAAACCCATTGTAAATTTACTTTGAAATGGAGGAATAAGTAAGTTATAAACGCGGGCTa                                                              >  1:235604/1‑141 (MQ=255)                                                                           aaCTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGAATAACTAAGTTATAAGCGCGTGCTAATCTCGTTATAg                                                  >  1:193984/1‑141 (MQ=255)                                                                                ccACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGAATAACTAAGTTATAAGCGCGTGCTGATCTCGTTATAGAATcg                                             >  1:145211/1‑140 (MQ=255)                                                                                    ccGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGAATAACTAAGTTATAAGCGCGTGCTAATCTCGTTATAGAATCCATTa                                         >  1:152441/1‑141 (MQ=255)                                                                                         tCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTATGTATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGAGGAATAACTAAGTTATAAGCGCGTGCTAATCTCGATATAGAATCCATTAAaata                                    <  1:325346/141‑1 (MQ=255)                                                                                          cAATATTTCTCGCTGCACCGAAGAATGCTTTTCGTTTGTGTATAGATGCAGGATCTAAACCAGCTGATAATGTACGACCACTTGGTGGAATAACTAAGTTATAAGCGCGTGCTAATCTCGTTATAGAATCCATTAAaataa                                   >  1:359287/1‑141 (MQ=255)                                                                                                       tGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGAATAACTAAGTTATAAGCGCGTGCTAATCTCGTTATAGAATCCATTAAAATAATGACATCTTcccc                      <  1:12475/141‑1 (MQ=255)                                                                                                                    gCTTTTGGTTTGTGTATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGAATAACTAAGTTATAAGCGCGTGCTAATCTCGTTATAGAATCCATTAAAATAATGACATCTTCCCCAATTTCTACTaaa         <  1:277148/141‑1 (MQ=255)                                                                                                                           gTTTGTGTATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGAATAACTAAGTTATAAGCGCGTGCTAATCTCGTTATAGAATCCATTAAAATAATGACATCTTCCCCAATTTCTACTAAACGCTTTg  <  1:216264/141‑1 (MQ=255)                                                                                                                                    |                                                                                                                                    TCCTTTAAATTCTTCGTAAATCATATCGTCCATACGTGAACCCGTATCAACTAATGCAGTTGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTAAAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGAATAACTAAGTTATAAGCGCGTGCTAATCTCGTTATAGAATCCATTAAAATAATGACATCTTCCCCAATTTCTACTAAACGCTTTG  >  USA300TCH1516_ALE/2236725‑2236987

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: ‑