Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_004302	2,759	0	C	T	33.3%	34.1 / 17.5	37	intergenic (‑2/‑228)	rro/tec	Repressor protein/tec
Reads supporting (aligned to +/- strand):  ref base C (0/24);  new base T (0/12);  total (0/37)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

CTCTTTCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑A‑C‑ACTAATTATAG  >  NC_004302/2689‑2770                                                                           |             ctctTTCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑a‑ctagt          <  1:16930199/75‑5 (MQ=255) ctctTTCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑a‑ctagt          <  1:4846492/75‑5 (MQ=255)  tctTTCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTTA‑T‑a‑c‑aaaaa        <  1:9268923/75‑5 (MQ=255)  tctTTCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑a‑ctaaac         <  1:14941615/75‑6 (MQ=255)     ttCATCGTCCACCCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑a‑c‑aaatcgcc     <  1:6204485/75‑8 (MQ=255)     ttCATCGTCCAACTATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑a‑c‑agcaagtt     <  1:5263548/75‑8 (MQ=255)     ttCATCGTCCAACCATTCTCTTTTCTGAATTAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑a‑c‑aaccgttg     <  1:3461452/75‑8 (MQ=255)     ttCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑t‑c‑accctcca     <  1:4715444/75‑7 (MQ=255)     ttCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑g‑c‑accttaga     <  1:1906676/75‑7 (MQ=255)     ttCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑g‑c‑acatatcc     <  1:5679361/75‑7 (MQ=255)     ttCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑g‑c‑acagcctt     <  1:4532786/75‑7 (MQ=255)     ttCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑g‑c‑acagcctt     <  1:14025296/75‑7 (MQ=255)     ttCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑c‑c‑acctcgcg     <  1:6433808/75‑7 (MQ=255)     ttCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑c‑c‑accaaatt     <  1:7685232/75‑7 (MQ=255)     ttCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑c‑c‑acaatggc     <  1:16214295/75‑7 (MQ=255)     ttCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑a‑c‑attgtttc     <  1:4706757/75‑8 (MQ=255)     ttCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑a‑c‑atattagt     <  1:13532295/75‑8 (MQ=255)     ttCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑a‑c‑ataccgtc     <  1:950783/75‑8 (MQ=255)     ttCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑a‑c‑aggaagat     <  1:7762037/75‑8 (MQ=255)     ttCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑a‑c‑agaacgtg     <  1:12337332/75‑8 (MQ=255)     ttCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑a‑c‑acctaagt     <  1:5845577/75‑7 (MQ=255)     ttCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑a‑c‑aagctcaa     <  1:1126069/75‑8 (MQ=255)     ttCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑a‑c‑aactccat     <  1:1802051/75‑8 (MQ=255)     ttCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑a‑c‑aaaaattt     <  1:13619132/75‑8 (MQ=255)     ttCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑a‑c‑aaaaattt     <  1:10972650/75‑8 (MQ=255)     ttCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑AGC‑ACTaagc      <  1:7228466/75‑3 (MQ=255)     ttCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑A‑T‑ACttcaaa     <  1:6697954/75‑6 (MQ=255)     ttCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑A‑T‑ACtctctt     <  1:11401587/75‑6 (MQ=255)     ttCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑A‑T‑ACtcacaa     <  1:15457756/75‑6 (MQ=255)     ttCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑A‑T‑ACTatcgt     <  1:16463328/75‑5 (MQ=255)     ttCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑A‑T‑ACTatatc     <  1:14217094/75‑5 (MQ=255)     ttCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑A‑T‑ACTaacct     <  1:5431755/75‑4 (MQ=255)     ttCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑A‑G‑ACtgcgtc     <  1:7711832/75‑6 (MQ=255)     ttCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑A‑C‑TCTattcg     <  1:14134283/75‑5 (MQ=255)     ttCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑A‑C‑CCTatata     <  1:11801597/75‑5 (MQ=255)     ttCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑A‑C‑CCTaccca     <  1:5002964/75‑5 (MQ=255)     ttCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑A‑C‑ACTatgtc     <  1:10936380/75‑5 (MQ=255)     ttCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑‑‑C‑ACTaagatg    <  1:6840447/75‑5 (MQ=255)     tccATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑A‑T‑ACtttccc     <  1:7976311/73‑6 (MQ=255)      tcatcaTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑c‑c‑acccaaaat    <  1:13551179/75‑8 (MQ=255)      tCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTATTTTTTTTCA‑T‑a‑c‑attcgtct     <  1:13420687/75‑8 (MQ=255)      tCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTATTTTTTTTCA‑T‑a‑c‑acagtcaa     <  1:5104899/75‑7 (MQ=255)      tCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTTA‑T‑A‑C‑ACTacctct    <  1:9684266/75‑6 (MQ=255)      tCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑c‑c‑acaacagcg    <  1:11822587/75‑8 (MQ=255)      tCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑a‑c‑acgcccttc    <  1:17252037/75‑8 (MQ=255)      tCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑a‑c‑acccaaaga    <  1:7455314/75‑8 (MQ=255)      tCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑a‑c‑acatctaac    <  1:17124219/75‑8 (MQ=255)      tCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑a‑c‑acactatct    <  1:13266421/75‑8 (MQ=255)      tCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑A‑CTACTaacca     <  1:14345184/75‑4 (MQ=255)      tCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑A‑C‑TCTaccacc    <  1:9795190/75‑6 (MQ=255)      tCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑A‑C‑‑CTAAttcaa   <  1:9058890/75‑4 (MQ=255)      tCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCATA‑TTTTTTTCA‑T‑A‑C‑TCTattgat    <  1:1876346/75‑6 (MQ=255)       cATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTTA‑T‑A‑C‑TCTagaccat   <  1:6062348/75‑7 (MQ=255)       cATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCATT‑A‑C‑ACTatatac    <  1:4842141/75‑6 (MQ=255)       cATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑TCA‑C‑ACtggacca    <  1:7105907/75‑7 (MQ=255)       cATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑G‑C‑ACtgctcgca   <  1:13090675/75‑8 (MQ=255)       cATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑C‑C‑ACtcgcttaa   <  1:5881816/75‑8 (MQ=255)       cATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑C‑C‑ACtcgatata   <  1:9197177/75‑8 (MQ=255)       cATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑A‑T‑ACTagcaaac   <  1:10140344/75‑7 (MQ=255)       cATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑A‑T‑ACTacctcgc   <  1:9804932/75‑7 (MQ=255)       cATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑A‑T‑ACTacctcgc   <  1:12786903/75‑7 (MQ=255)       cATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑A‑T‑ACTaccctcc   <  1:14118491/75‑7 (MQ=255)       cATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑A‑C‑CCTattgctt   <  1:130290/75‑7 (MQ=255)       cATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑A‑C‑CCTaagatac   <  1:5112203/75‑6 (MQ=255)       cATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑‑‑C‑ACTacccgtgc  <  1:5322708/75‑8 (MQ=255)       cATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑‑‑C‑ACTaagggaac  <  1:5616196/75‑7 (MQ=255)        aTCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTATTTTTTTTCA‑T‑A‑T‑ACTacctact   <  1:3623500/75‑7 (MQ=255)        aTCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑A‑C‑TCTacatgatt  <  1:9463036/75‑8 (MQ=255)        aTCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑A‑C‑CCTacaacatc  <  1:5551559/75‑8 (MQ=255)        aTCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑A‑C‑CCTAAtctatc  <  1:17214147/75‑6 (MQ=255)                                                                           |             CTCTTTCATCGTCCAACCATTCTCTTTTCTGAAATAATCTATCATTTCAGGTAGTCGTA‑TTTTTTTCA‑T‑A‑C‑ACTAATTATAG  >  NC_004302/2689‑2770

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑