Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	3,960,035	C→G	36.7%	R87G (CGC→GGC)	rho →	transcription termination factor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	3,960,035	0	C	G	36.7%	18.0 / 19.7	26	R87G (CGC→GGC)	rho	transcription termination factor
Reads supporting (aligned to +/- strand):  ref base C (11/4);  new base G (3/6);  total (15/11)
Fisher's exact test for biased strand distribution p-value = 9.18e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.51e-01

CATCCTGAAGCAGCACGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGGATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTC‑CTGATGACATCTACGTTTCCCCTAGCCAAATCCGCCGTTTCAACCTCCGCACTGGTGATACCATCTCTGGTAAGATTCGCCCGCCGAAAGAAGGTGAACGCTATTTTGCGCTGCTGAAAGTTAACGAAGTTAACTTCGACAAACCTGAAAACGCCCGCAACAAAATCCTCTTTGAGAACT  >  CP009273/3959887‑3960182                                                                                                                                                      |                                                                                                                                                    cATCCTGAAGCAGCACGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCGGGATGGATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTC‑CTGATGACATCTACGTTTCCCCTAGCCAAATcc                                                                                                                                                     >  2:308605/1‑149 (MQ=255)   tCCTGAAGCAGCTCGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGGATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTC‑CTGATGACATCTACGTTTCCCCTAGCCAAATcggc                                                                                                                                                   <  2:3393/149‑1 (MQ=255)   tCCTGAAGCAGCACGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGGATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTC‑CTGATGACATCTACGTTTCCCCTAGCCAAATcggc                                                                                                                                                   >  2:140052/1‑149 (MQ=255)            agcaCGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGGATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCAGGTC‑CGGGTGACATCTACGTTTCCCCTAGCCAAATCGGCCGTTTCAAc                                                                                                                                          >  2:155985/1‑149 (MQ=255)               aCGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGGATTTGGTTTCCTGCGTTCCGCAGACAGCTCCTACCTCGCCGGTC‑CTGATGACATCTACGTTTCCCCTAGCCAAATCCGCCGTTTCAACCTc                                                                                                                                       >  2:340517/1‑149 (MQ=255)                          ggggAAGATAGCTTTGGTGGTGGCGGACTGGAGATATTGCAGGATGGATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTC‑CTGATGACATCTACGTTTCCCCTAGCCAAATCAGCCGTTTCAACCTCCGCACTGGTGa                                                                                                                            <  1:199383/146‑1 (MQ=255)                          ggCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGGATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTC‑CTGATGACATCTACGTTTCCCCTAGCCAAATCGGCCGTTTCAACCTCCGCACTGGTGa                                                                                                                            <  2:275551/149‑1 (MQ=255)                          ggCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGGATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTC‑CTGATGACATCTACGTTTCCCCTAGCCAAATCCGCCGTTTCAACCTCCGCACTGGTGa                                                                                                                            <  1:156119/149‑1 (MQ=255)                                      tttGGTGATGGCGTACTGGAGATATTGCAGGATGGATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTC‑CTGATGACATCTACGTTTCCCCTAGCCAAATCGGCCGTTTCAACCTCCGCACTGGTGATACCATCTCTgg                                                                                                                >  2:62861/1‑149 (MQ=255)                                       ttGGTGATGGCGTACTGGAGATATTGCAGGATGGATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTC‑CTGATGACATCTACGTTTCCCCTAGCCAAATCGGCCGTTTCAACCTCCGCACTGGTGATACCATCTCTGGt                                                                                                               <  2:59891/149‑1 (MQ=255)                                            gATGGCGTACTGGAGATATTGCAGGATGGATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTC‑CTGATGACATCTACGTTTCCCCTAGCCAAATCAGCCGTTTCAACCTCCGCACTGGTGATACCATCTCTGGTAAAAt                                                                                                          >  1:73525/1‑149 (MQ=255)                                              tGGCGTACTGGAGATATTGCAGGATGGATTTGGTCTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTC‑CTGATGACATCTACGTTTCCCCTAGCCAAATCCGCCGTTTCAACCTCCGCACTGGTGATACCATCTCTGGTAAGATTc                                                                                                        <  2:317035/149‑1 (MQ=255)                                               ggCGTACTGGAGATATTGCAGGATGGATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTC‑CTGATGACATCTACGTTTCCCCTAGCCAAATCCGCCGTTTCAACCTCCGCACTGGTGATACCATCTCTGGTAAGATTcg                                                                                                       >  1:181363/1‑149 (MQ=255)                                                          gaTATTGCAGGATGGATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTC‑CTGATGACATCTACGTTTCCCCTAGCCAAATCCGCCGTTTCAACCTCCGCACTGGTGATACCATCTCTGGTAAGATTCGCCCGCCGAaag                                                                                            >  2:248864/1‑149 (MQ=255)                                                          gaTATTGCAGGAGGGATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGACGGTC‑CTGGTGACATCTACGTTTCCCCTAGCCAAATCCGCCGGTTCAACCTCCGCACTGGTGATACCATCACTGGTCAGGTTGCCCCGCCCaaac                                                                                            >  1:4291/1‑148 (MQ=255)                                                             atTGCAGGATGGATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTC‑CTGATGACATCTACGTTTCCCCTAGCCAAATCGGCCGTTTCAACCTCCGCACTGGTGATACCATCTCTGGTAAGATTCGCCCGCCGAaagaag                                                                                         >  2:119701/1‑149 (MQ=255)                                                                             ggTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGGC‑CTGATGACCTCTACCTTTCCCCTAGCCAAATCCCCCGGTTCCACCTCCCCACTGGGGATAACATCCCTCGGCAGATTCCCCCCCCGAAAGAACGTGACCgaacttttga                                                                         >  1:26509/1‑140 (MQ=255)                                                                                  cctccGTTCGCCAGACACCTCCTACCTCGCCGGTC‑CTGATGACATCTACGTTTCCCCTAGCCAAATCCGCCGTTTCAACCTCCGCACTGGTGATACCATCTCTGGTAAGATTCGCCCGCCGAAAGAAGGTGAACGCTATTTTGCgctgc                                                                    <  1:340517/149‑1 (MQ=255)                                                                                   ctccGTTCCGCAGACAGCTCCTACCTAACAGGTCGCAGA‑GTGATCTACGTTTCCCCTAGCCAAATCCGCCGTTTCAACCTCCGCACTGGTGATACCATCTCTGGTAAGATTCGCCCGCCGAAAGAAGGTGAACGCGATTTTGCgctgct                                                                   >  2:174824/1‑149 (MQ=255)                                                                                          ccGCAGACAGCTCCTACCTCGCCGGTC‑CTGATGACATCTACGTTTCCCCTAGCCAAATCGGCCGTTTCAACCTCCGCACTGGTGATACCATCTCTGGTAAGATTCGCCCGCCGAAAGAAGGTGAACGCTATTCTGCGCTGCTGAAAGtt                                                            <  2:224014/149‑1 (MQ=255)                                                                                                  aGCTCCTACCTCGCCGGTC‑CTGATGACATCTACGTTTCCCCTAGCCAAATCGGCCGTTTCAACCTCCGCACTGGTGATACCATCTCTGGTAAGATTCGCCCGCCGAAAGAAGGTGAACGCTATTTTGCGCTGCTGAAAGTTAACGAAGt                                                    <  2:268203/149‑1 (MQ=255)                                                                                                       cTACCTCGCCGGTC‑CTGATGACATCTACGTTTCCCCTAGCCAAATCCGCCGTTTCAACCTCCGCACTGGTGATACCATCTCTGGTAAGATTCGCCCGCCGAAAGAAGGTGAACGCTATTTTGCGCTGCTGAACGTTAACGAAGTTAACt                                               >  2:343555/1‑149 (MQ=255)                                                                                                            tCGCCGGTC‑CTGATGACATCTACGTTTCCCCTAGCCAAATCCGCCGTTTCAACCTCCGCACTGGTGATACCATCTCTGGTAAGATTCGCCCGCCGAAAGAAGGTGAACGCTATTTTGCGCTGCTGAAAGTTAACGAAGTTAACTTCGAc                                          >  2:209727/1‑149 (MQ=255)                                                                                                                         acgaCATCTGCGTTTCCCCTAGCCAAATCCGCCGTTTCAACCTCCGCACTGGTGATACCCTCTCTGGTAAGATTCGCCCGCCGAAAGAAGGTGAACGCTATTTTGCGCTGCTGAAAGTTAACGAAGTTAACTTCGACAAACCTGAAAAc                              <  2:346991/147‑1 (MQ=255)                                                                                                                               tCTACGTTTCCCCTAGCCAAATCCGCCGTTTCAACCTCCGCACTGGTGATACCATCTCTGGTAAGATTCGCCCGCCGAAAGAAGGTGAACGCTATTTTGCGCTGCTGAAAGTTAACGAAGTTAACTTCGACAAACCTGAAAACGCCCGc                        >  2:124719/1‑149 (MQ=255)                                                                                                                                cTACGTTTCCCCTAGCCAAATCCGCCGTTTCAACCTCCGCACTGGTGATACCATCTCTGGTAAGATTCGCCCGCCGAAAGAAGGTGAACGCTATTTTGCGCTGCTGAAAGTTAACGAAGTTAACTTCGACAAACCTGAAAACGCCCGca                       >  1:181418/1‑149 (MQ=255)                                                                                                                                        tccccctccAAAGCGGCCGTTTCAACCTCCGCCCTGGTGATTCCCTCTCTGCTAACACTCGTCCGCCGAAAGAATGTGACCGCTATTTTTCGCTTCTGAAAGACAACGAATTTAACTACGACAAACCTGAAAACGCCCTCATCAAAATc               <  1:64599/142‑1 (MQ=255)                                                                                                                                         cccTAGCCAAATCCGCCGTTTCAACCTCCGAACTGGTGATACCAACTCTGGTAAGATTCGCCCGCCGAAAGAAGGTGAACGCTATTTTGCGCTGCTGAAAGTTAACGCAGTTAACTTCTACAACCCAGAAAACGCCCGCCACAAAAtac              >  1:272880/1‑147 (MQ=255)                                                                                                                                                cAAATCGGCCGTTTCAACCTCCGCACTGGTGATACCATCTCTGGTAAGATTCGCCCGCCGAAAGAAGGTGAACGCTATTTTGCGCTGCTGAAAGTTAACGAAGTTAACTTCGACAAACCTGAAAACGCCCGCAACAAAATCCTCTTTga       <  1:119701/149‑1 (MQ=255)                                                                                                                                                     ccgccgTTTCAACCTCCGCACTGGTGATACCATCTCTGGTAAGATTCGCCCGCCGAAAGAAGGTGAACGCTATTTTGCGCTGCTGAAAGTTAACGAAGTTAACTTCGACAAACCTGAAAACGCCCGCAACAAAATCCTCTTTGAGAACt  <  1:235610/149‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                                    CATCCTGAAGCAGCACGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGGATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTC‑CTGATGACATCTACGTTTCCCCTAGCCAAATCCGCCGTTTCAACCTCCGCACTGGTGATACCATCTCTGGTAAGATTCGCCCGCCGAAAGAAGGTGAACGCTATTTTGCGCTGCTGAAAGTTAACGAAGTTAACTTCGACAAACCTGAAAACGCCCGCAACAAAATCCTCTTTGAGAACT  >  CP009273/3959887‑3960182

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑