Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,454,461	C→T	W313* (TGG→TAG)	gspA ←	Type II secretion system protein GspA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,454,461	0	C	T	100.0%	108.4 / NA	30	W313* (TGG→TAG)	gspA	Type II secretion system protein GspA
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (9/21);  total (9/21)

AAATTCTGATCTACCAATGTTTGTAAAGAAGCATTCCCACTTTTACATGCCAGCCCCGCTCTTACTGCCTGATCGCACCAGGCCGAATCAGCTGGGACCTCGTACCCCCATACGCCGTATAACACGCTTAGCGCCTCACTATCGCGCATCACCAC  >  NC_000913/3454383‑3454537                                                                               |                                                                             aaaTTCTGATCTACCAATGTTTGTAAAGAAGCATTCCCACTTTTACATGCCAGCCCCGCTCTTACTGCCTGATCGCACTAg                                                                            <  1:650538/81‑1 (MQ=255)   aTTCTGATCTACCAATGTTTGTAAAGAAGCATTCCCACTTTTACATGCCAGCCCCGCTCTTACTGCCTGATCGCACTAGGc                                                                          <  2:650539/81‑1 (MQ=255)        gATCTACCAATGTTTGTAAAGAAGCATTCCCACTTTTACATGCCAGCCCCGCTCTTACTGCCTGATCGCACTAGGCCGAAt                                                                     >  2:650572/1‑81 (MQ=255)         aTCTACCAATGTTTGTAAAGAAGCATTCCCACTTTTACATGCCAGCCCCGCTCTTACTGCCTGATCGCACTAGGCCGAAt                                                                     <  1:650540/80‑1 (MQ=255)          tCTACCAATGTTTGTAAAGAAGCATTCCCACTTTTACATGCCAGCCCCGCTCTTACTGCCTGATCGCACTAGGCCGAAt                                                                     >  1:650588/1‑79 (MQ=255)                    tttGTAAAGAAGCATTCCCACTTTTACATGCCAGCCCCGCTCTTACTGCCTGATCGCACTAGGCCGAATCAGCTGGGAcc                                                          <  1:650541/80‑1 (MQ=255)                    tttGTAAAGAAGCATTCCCACTTTTACATGCCAGCCCCGCTCTTACTGCCTGATCGCACTAGGCCGAATCAGCTGGGACCt                                                         <  1:650542/81‑1 (MQ=255)                     ttGTAAAGAAGCATTCCCACTTTTACATGCCAGCCCCGCTCTTACTGCCTGATCGCACTAGGCCGAATCAGCTGGGACCTc                                                        >  1:650591/1‑81 (MQ=255)                       gTAAAGAAGCATTCCCACTTTTACATGCCAGCCCCGCTCTTACTGCCTGATCGCACTAGGCCGAATCAGCTGGGACCTCg                                                       <  1:650544/80‑1 (MQ=255)                       gTAAAGAAGCATTCCCACTTTTACATGCCAGCCCCGCTCTTACTGCCTGATCGCACTAGGCCGAATCAGCTGGGACCTCg                                                       <  2:650543/80‑1 (MQ=255)                        tAAAGAAGCATTCCCACTTTTACATGCCAGCCCCGCTCTTACTGCCTGATCGCACTAGGCCGAATCAGCTGGGACCTCGt                                                      <  1:650545/80‑1 (MQ=255)                              agCATTCCCACTTTTACATGCCAGCCCCGCTCTTACTGCCTGATCGCACTAGGCCGAATCAGCTGGGACCTCGTACCCCCa                                               <  2:650546/81‑1 (MQ=255)                                 aTTCCCACTTTTACATGCCAGCCCCGCTCTTACTGCCTGATCGCACTAGGCCGAATCAGCTGGGACCTCGTACCCCCATAc                                            <  2:650547/81‑1 (MQ=255)                                        cTTTTACATGCCAGCCCCGCTCTTACTGCCTGATCGCACTAGGCCGAATCAGCTGGGACCTCGTACCCCCATACGCCGta                                      >  2:650586/1‑80 (MQ=255)                                                   cAGCCCCGCTCTTACTGCCTGATCGCACTAGGCCGAATCAGCTGGGACCTCGTACCCCCATACGCCGTATAACACGCTTAg                          <  2:650548/81‑1 (MQ=255)                                                    aGCCCCGCTCTTACTGCCTGATCGCACTAGGCCGAATCAGCTGGGACCTCGTACCCCCATACGCCGTATAACACGCTTAgc                         <  2:650549/81‑1 (MQ=255)                                                      ccccGCTCTTACTGCCTGATCGCACTAGGCCGAATCAGCTGGGACCTCGTACCCCCATACGCCGTATAACACGCTTAgcgc                       >  1:650582/1‑81 (MQ=255)                                                      ccccGCTCTTACTGCCTGATCGCACTAGGCCGAATCAGCTGGGACCTCGTACCCCCATACGCCGTATAACACGCTTAgcgc                       <  1:650550/81‑1 (MQ=255)                                                              ttACTGCCTGATCGCACTAGGCCGAATCAGCTGGGACCTCGTACCCCCATACGCCGTATAACACGCTTAGCGCCTCACt                 <  1:650551/79‑1 (MQ=255)                                                                aCTGCCTGATCGCACTAGGCCGAATCAGCTGGGACCTCGTACCCCCATACGCCGTATAACACGCTTAGCGCCTCACTAt               <  1:650552/79‑1 (MQ=255)                                                                aCTGCCTGATCGCACTAGGCCGAATCAGCTGGGACCTCGTACCCCCATACGCCGTATAACACGCTTAGCGCCTCACTATcg             >  2:650581/1‑81 (MQ=255)                                                                aCTGCATGATCGCACTAGGCCGAATCAGCTGGGACCTCGTACCCCCATACGCCGTATAACACGCTTAGCGCCTCACTATc              <  1:650553/80‑1 (MQ=255)                                                                 cTGCCTGATCGCACTAGGCCGAATCAGCTGGGACCTCGTACCCCCATACGCCGTATAACACGCTTAGCGCCTCACTATcgc            <  2:650554/81‑1 (MQ=255)                                                                   gCCTGATCGCACTAGGCCGAATCAGCTGGGACCTCGTACCCCCATACGCCGTATAACACGCTTAGCGCCTCACTATcgcg           >  2:650587/1‑80 (MQ=255)                                                                    ccTGATCACACTTGGCCGAATCAGCTGGGACCTCGTACCCCCATACACCGTATAACACGCTTAGCGCCTCACTATCgcgc          <  1:650555/80‑1 (MQ=255)                                                                       gATCGCACTAGGCCGAATCAGCTGGGACCTCGTACCCCCATACGCCGTATAACACGCTTAGCGCCTCACTATCGCGCATca      >  2:650593/1‑81 (MQ=255)                                                                       gATCGCACTAGGCCGAATCAGCTGGGACCTCGTACCCCCATACGCCGTATAACACGCTTAGCGCCTCACTATCGCGCATca      >  2:650589/1‑81 (MQ=255)                                                                        aTCGCACTAGGCCGAATCAGCTGGGACCTCGTACCCCCATACGCCGTATAACACGCTTAGCGCCTCACTATCGCGCATcac     <  1:650556/81‑1 (MQ=255)                                                                           gCACTAGGCCGAATCAGCTGGGACCTCGTACCCCCATACGCCGTATAACACGCTTAGCGCCTCACTATCGCGCATcaccac  <  2:650557/81‑1 (MQ=255)                                                                           gCACTAGGCCGAATCAGCTGGGACCTCGTACCCCCATACGCCGTATAACACGCTTAGCGCCTCACTATCGCGCATcacca   <  2:650558/80‑1 (MQ=255)                                                                               |                                                                             AAATTCTGATCTACCAATGTTTGTAAAGAAGCATTCCCACTTTTACATGCCAGCCCCGCTCTTACTGCCTGATCGCACCAGGCCGAATCAGCTGGGACCTCGTACCCCCATACGCCGTATAACACGCTTAGCGCCTCACTATCGCGCATCACCAC  >  NC_000913/3454383‑3454537

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑