Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,038,807	0	C	A	75.6%	13.9 / 34.1	45	noncoding (1289/2905 nt)	rrlA	23S ribosomal RNA of rrnA operon
Reads supporting (aligned to +/- strand):  ref base C (4/7);  new base A (18/16);  total (22/23)
Fisher's exact test for biased strand distribution p-value = 4.91e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.03e-01

CCATGCACCGAAGCTGCGGCAGCGACACTATGTGTTGTTGGGTAGGGGAGCGTTCTGTAAGCCTGTGAAGGTGTGCTGTGAGGCATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAGGGTTCCTGTCCAACGTTAATCGGGGCAGGGTGAGTCGACCC  >  NC_000913/4038663‑4038867                                                                                                                                                 |                                                             ccATGCACCGAAGCTGCGGCAGCGACACTATGTGTTGTTGGGTAGGGGAGCGTTCTGTAAGCCTGTGAAGGTGTGCTGTGAGGCATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCg                                                        <  2:542539/151‑1 (MQ=39)     gCACCGAAGCTGCGGCAGCGACACTATGTGTTGTTGGGTAGGGGAGCGTTCTGTAAGCCTGTGAAGGTGTGCTGTGAGGCATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCgg                                                    <  2:387085/151‑1 (MQ=39)          gAAGCTGCGGCAGCGACACTATGTGTTGTTGGGTAGGGGAGCGTTCTGTAAGCCTGTGAAGGTGTGCTGTGAGGCATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGAc                                               >  2:586312/1‑151 (MQ=39)                 cGGCAGCGACACTATGTGTTGTTGGGTAGGGGAGCGTTCTGTAAGCCTGTGAAGGTGTGCTGTGAGGCATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAGGGt                                        >  2:268130/1‑151 (MQ=39)                    cAGCGACACTATGTGTTGTTGGGTAGGGGAGCGTTCTGTAAGCCTGTGAAGGTGTGCTGTGAGGCATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAGGGTTcc                                     <  1:33674/151‑1 (MQ=39)                             cgtaagtgacgcggTAGAGGAGCGTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAgc                                          <  2:451022/125‑2 (MQ=2)                             cgtaagtgacgcggTAGAGGAGCGTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAgc                                          >  1:451074/13‑136 (MQ=2)                             cgcaagtgacgcggTAGAGGAGCGTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAgg                                          <  1:331104/125‑1 (MQ=2)                             cgcaagtgacgcggTAGAGGAGCGTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAgg                                          >  2:331064/13‑137 (MQ=2)                             cgcaagtgacgcggTAGAGGAGCGTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAGGGTTCCTGCGCAACg                            >  1:522501/13‑151 (MQ=2)                                  gttgttGGGTAGGGGAGCGTTCTGTAAGCCTGTGAAGGTGTGCTGTGAGGCATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAGGGTTCCTGTCCAACGTTaa                        <  2:31878/150‑1 (MQ=31)                                    gacgcggTAGAGGAGCGTTCTGTAAGCCTGTGAAGGTGAGTTG‑AAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAGGGTTCCTGCGCAACGTTAATCg                     >  2:649077/6‑150 (MQ=2)                                      ttgGGTAGGGGAGCGTTCTGTAAGCCTGTGAAGGTGTGCTGTGAGGCATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAGGGTTCCTGTCCAACGTTAATCggg                   >  1:694417/1‑151 (MQ=31)                                         ggTAGAGGAGCGTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAGGGTTCCTGCGCAACGTTAATCgacgc                 >  1:565988/1‑146 (MQ=2)                                          gTAGAGGAGCGTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAg                                                 <  1:320927/117‑1 (MQ=2)                                          gTAGAGGAGCGTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAg                                                 >  2:320888/1‑117 (MQ=2)                                           tAGAGGAGCGTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAGGGTTCCTGCGCAACGTTAATCgacg                  <  1:31279/147‑4 (MQ=2)                                           tAGAGGAGCGTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAGGGTTCCTGCGCAACGTTAATCgacg                  >  2:31275/1‑144 (MQ=2)                                            aGGGGAGCGTTCTGTAAGCCTGTGAAGGTGTGCTGTGAGGCATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAGGGTTCCTGTCCAACGTTAATCGGGGCAggg             <  1:341675/151‑1 (MQ=31)                                              aggAGCGTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAGGGTTCCTgcgc                                <  1:347078/129‑4 (MQ=11)                                              aggAGCGTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAGGGTTCCTgcgc                                >  2:347037/2‑127 (MQ=11)                                                gAGCGTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAATACCCACGCCGAAAGACCAAg                                           <  2:6396/117‑1 (MQ=2)                                                gAGCGTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAATACCCACGCCGAAAGACCAAg                                           >  1:6396/1‑117 (MQ=2)                                                gAGCGTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAg                                           <  1:172942/117‑1 (MQ=2)                                                gAGCGTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAg                                           >  2:172924/1‑117 (MQ=2)                                                 aGCGTTCTGTAAGCCTGTGAAGGTGTGCTGTGAGGCATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAGGGTTCCTGTCCAACGTTAATCGGGGCAGGGTGAGt        <  1:331710/151‑1 (MQ=31)                                                  gCGTTCTGTAAGCCTGTGAAGGTGTGCTGTGAGGCATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAGGGTTCCTGTCCAACGTTAATCGGGGCAGGGTGAGTc       <  1:666725/151‑1 (MQ=31)                                                  gCGTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCaa                                            <  1:369661/114‑1 (MQ=2)                                                  gCGTTCTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCaa                                            >  2:369618/1‑114 (MQ=2)                                                     ttCTGTAAGCCTGTGAAGGTGTGCTGTGAGGCATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAGGGTTCCTGTCCAACGTTAATCGGGGCAGGGTGAGTCGAc    >  1:20630/1‑151 (MQ=31)                                                       cTGTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAGGGTTCCTGCGCAACGTTAATCGACGCAGGGTTAGTCggttc  >  1:368788/1‑147 (MQ=2)                                                         gTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAgg                                          >  1:192692/1‑109 (MQ=2)                                                         gTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAgg                                          <  2:192672/109‑1 (MQ=2)                                                         gTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAGGGTTCCTGCGCAACGTTAATCGACGCAGGGTTAGttggttt  <  2:565923/149‑7 (MQ=2)                                                         gTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAGGGTTCCTGCGCAACGTTAATCGACGCAGGGTTAGTCggttc  <  2:522440/149‑5 (MQ=2)                                                         gTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCAGAAAGACCAAg                                           >  2:337243/1‑108 (MQ=2)                                                         gTAAGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCAGAAAGACCAAg                                           <  1:337283/108‑1 (MQ=2)                                                            aGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCaa                                            >  1:103738/1‑104 (MQ=2)                                                            aGCCTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCaa                                            <  2:103726/104‑1 (MQ=2)                                                               cTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAgg                                          <  1:578779/103‑1 (MQ=2)                                                               cTGTGAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAgg                                          >  2:578712/1‑103 (MQ=2)                                                                 gtgAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAg                                                 >  2:393364/1‑94 (MQ=2)                                                                 gtgAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAg                                                 <  1:393407/94‑1 (MQ=2)                                                                 gtgAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAGGGTTCCTGCGCAACGTTAATCGACGCAGGGTTAGTCggt    <  2:342122/139‑3 (MQ=2)                                                                 gtgAAGGTGAGTTGAGAAGCTTGCTGGAGGTATCAGAAGTGCGAATGCTGACATGAGTAACGACAATGGGTGTGAAAAACACCCACGCCGAAAGACCAAGGGTTCCTGCGCAACGTTAATCGACGCAGGGTTAGTCggt    >  1:342162/1‑137 (MQ=2)                                                                                                                                                 |                                                             CCATGCACCGAAGCTGCGGCAGCGACACTATGTGTTGTTGGGTAGGGGAGCGTTCTGTAAGCCTGTGAAGGTGTGCTGTGAGGCATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAGGGTTCCTGTCCAACGTTAATCGGGGCAGGGTGAGTCGACCC  >  NC_000913/4038663‑4038867

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑