Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	BS168_reference_genome	3,935,825	Δ1 bp	coding (1190/1191 nt)	rlmI ←	large subunit ribosomal RNA m5C1962 methyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	BS168_reference_genome	3,935,823	0	T	.	95.5%	172.0 / 3.3	45	intergenic (+35/+1)	ywbE/rlmI	conserved protein of unknown function/large subunit ribosomal RNA m5C1962 methyltransferase
Reads supporting (aligned to +/- strand):  ref base T (1/0);  major base . (24/18);  minor base A (2/0);  total (27/18)
Fisher's exact test for biased strand distribution p-value = 5.05e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.54e-01

TTTGACGAAATCAAACTTTCATCCGCATGGCATTAAAGTCCGTCTTGAAGATGGCCGCATCGGCCGCGACCAGCAGATCGTTTCTACATAAAAAAAAGCTGCCCCTGAACAGGGCAGCTTTTTCATTTATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGAAATCCTCCGGCAGCGTAAATTCCTCAATGATCGTGTAGCGTTCATTTGTTTCTTTAAAGGCGGCA  >  BS168_reference_genome/3935698‑3935953                                                                                                                              |                                                                                                                                   tttGACGAAATCAAACTTTCATCCGCATGGCATTAAAGTCCGTCTTGAAGATGGCCGCATCGGCCGCGACCAGCAGATCGTTTCTACATAAAAAAAAGCTGCCCCTGAACAGGGCAGCTTTTTCA‑TTATTTTTTCTg                                                                                                                        >  6:320675/1‑137 (MQ=255) tttGACGAAATCAAACTTTCATCCGCATGGCATTAAAGTCCGTCTTGAAGATGGCCGCATCGGCCGCGACCAGCAGATCGTTTCTACATAAAAAAAAGCTGCCCCTGAACAGGGCAGCTTTTTCA‑TTATTTTTTCTg                                                                                                                        >  3:128153/1‑137 (MQ=255) tttGACGAAATCAAACTTTCATCCGCATGGCATTAAAGTCCGTCTTGAAGATGGCCGCATCGGCCGCGACCAGCAGATCGTTTCTACATAAAAAAAAGCTGCCCCTGAACAGGGCAGCTTTTTCA‑TTATTTTTTATg                                                                                                                        >  6:2317/1‑137 (MQ=255)    gACTAAATCAAACTTACATCCGCTTGGATTTAAAGTCCGTCTTTACGAGGGCCGCTTCGCCCGCGACCAGCAGATCGTTTCTACATAAAAAAAAGCTGCCCCTGAACAGGGCAGCTTTTTCA‑TTATTTTTTCTGCAGa                                                                                                                    <  3:277388/138‑1 (MQ=255)     aCGAAATCAAACTTTCATCCGCATGGCATTAAAGTCCGTCTTGAAGATGGCCGCATCGGCCGCGACCAGCAGATCGTTTCTACATAAAAAAAAGCTGCAACTGAAAAGTGCAGCTTTTT‑AATTATTTTTTATTCAGAAg                                                                                                                  >  6:130517/1‑139 (MQ=255)          aTCAAACTTTCATCCGCATGGCATTAAAGTCCGTCTTGAAGATGGCCGCATCGGCCGCGACCAGCAGATCGTTTCTACATAAAAAAAAGCTGCCCCTGAACAGGGCAGCTTTTTCA‑TTATTTTTTCTGCAGAAGGcccc                                                                                                             >  3:207364/1‑138 (MQ=255)                                  tAAAGTCCGTCTTGAAGATGGCCGCATCGGCCGCGCCCAGCAGATCGTTTCTACATAAAAAAAAGCTGCCCCGGAACAGGGCAGCTTTTTCA‑TTATTTTTTCTGCAGAAGGACCACTTTCAGGTACTTGCCTTCCGGa                                                                                      >  2:155951/1‑138 (MQ=255)                                         cGTCTTGAAGATGGCCGCATCGGCCGCGACCAGCAGATCGTTTCTACATAAAAAAAAGCTGCCCCTGAACAGGGCAGCTTTTTCA‑TTATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTTCCTTCCGGAAATGCCg                                                                               >  3:219534/1‑138 (MQ=255)                                         cGTCTTGAAGATGGCCGCATCGGCCGCGACCAGCAGATCGTTTCTACATAAAAAAAAGCTGCCCCTGAACAGGGCAGCTTTTTCA‑TTATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCg                                                                               >  1:256528/1‑138 (MQ=255)                                         cGTCTTGAAGATGGACGCATCTTAAAAGACCAACAGATCGTTTCTACATAAAAAAAAGCTGCCCCAGAACAGGGCAGCTTTTT‑AATTAATTTTTCTGAAGAAGGACCACTTTAAGGTAGTTGCCTTCCGGAAATGccc                                                                               >  6:177952/1‑137 (MQ=255)                                         agTCTTGAAGATGGCCGCATCGGCCGCGACCAGCAGATCGTTTCTACATAAAAAAAAGCTGACCCAGAACACGGCAGCTTATTCA‑TTATTTTTTCTGCAGAAGTACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCg                                                                               >  6:67543/2‑138 (MQ=255)                                           tCTTGAAGATGGCCGCATCGGCCGCGACCAGCAGATCGTTTCTACATAAAAAAAAGCTGCCCCTGAACAGGGCAGCTTTTTCA‑TTATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGaaa                                                                            >  7:292963/1‑139 (MQ=255)                                               ctctgtGGCCGCATCGGCCGCGTCCAGAAGATCGTTTCTACATAAAAAAAAGCTGCCCCTGAACAGGGCAGCTTTTTCA‑TTATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCg                                                                         <  4:24824/133‑1 (MQ=255)                                                aaGCTGGCCGCATCGGCCGCGACCAGCAGATCGTTTCTACATAAAAAAAAGCTGCCCCAGCACAGGGCAGCTTTTTCA‑TTATTTTTTCTGGAGAAGGACCACGTTCACGTAGTTGCCTTCCGGAAGTGCCGAAATCGtt                                                                       >  3:342914/1‑139 (MQ=255)                                                    tGGCCGCATCGGCCGCGACCAGCAGATCGTTTCTACATAAAAAAAAGCTGCCCCTGAACAGGGCAGCTTTTTCA‑TTATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCTAAATCGTGTTg                                                                    >  4:229914/1‑138 (MQ=255)                                                    ggcccGCAGCGCCCGCGACCAGCAGATCGTTGCTACATAAAAAAAAGCTGCCCCTGAACAGGGCAGCTTTTTCA‑TTATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGa                                                                   <  6:292219/136‑1 (MQ=255)                                                     ggCCGCATCGGCCGCGACCAGCAGATCGTTTCTACATAAAAAAAAGCTGCCCCTGAACAGGGCAGCTTTTTCA‑TTATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATTCCGAAATCGTTTTGa                                                                   >  4:275586/1‑138 (MQ=255)                                                     ggCCGCATCGGCCGCGACCAGCAGATCGTTTCTACATAAAAAAAAGCTGCCCCTGAACAGGGCAGCTTTTTCA‑TTATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGa                                                                   >  1:29101/1‑138 (MQ=255)                                                                          cagATCGTTTCTACATAAAAAAAAGCTGCCCCTGAACAGGGCAGCTTTTTCA‑TTATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGAAATCCTCCGGCAGCGTAAATTc                                             >  7:155525/1‑139 (MQ=255)                                                                             aTCGTTTCTACATAAAAAAAAGCTGCCCCTGAACAGGGCAGCTTTTTCA‑TTATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGAAATCCTCCGGCAGCGTAAATTCCt                                           >  3:205848/1‑138 (MQ=255)                                                                               cGTTTCTACATAAAAAAAAGCTGCCCCTGAACAGGGCAGCTTTTTCA‑TTATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGAAATCCTCCGGCAGCGTAAATTCCTCaa                                        <  8:229308/139‑1 (MQ=255)                                                                               cGTTTCTACATAAAAAAAAGCTGCCCCTGAACAGGGCAGCTTTTTCA‑TTATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGAAATCCTCAGGCAGCGTAAATTCCTCaa                                        >  4:56120/1‑139 (MQ=255)                                                                                gTTTCTACATAAAAAAAAGCTGCCCCTGAACAGGGCAGCTTTTTCA‑TTATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGAAATCCTCCGGCAGCGTAAATTCCTCaa                                        <  4:205848/138‑1 (MQ=255)                                                                                gTTTCTACATAAAAAAAAGCTGCCCCTGAACAGGGCAGCTTTTTCA‑TTATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGAAATCCTCCGGCAGCGTAAATTCCTCaa                                        <  4:219534/138‑1 (MQ=255)                                                                                gTTTATAAATAAAAAAAAGCTGCCCCTGAACAGGGCAGCTTTTTCA‑TTATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGAAATCCTCCTGCAGCGTAAATTCCTCaa                                        <  5:130517/138‑1 (MQ=255)                                                                                       cATAAAAAAAAGCTGCCCCTGAACAGGGCAGCTTTTTCA‑TTATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGAAATCCTCCGGCAGCGTAAATTCCTCAATg                                      >  1:250454/1‑133 (MQ=255)                                                                                       cATAAAAAAAAGCTGCCCCTGAACAGGGCAGCTTTTTCA‑TTATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGAAATCCTCCGGCAGCGTAAATTCCTCAATg                                      <  2:250454/133‑1 (MQ=255)                                                                                        cataaaaaaaGCTGCCCCTGAACAGGGCAGCTTTTTCA‑TTATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGAAATCCTCCGGCAGCGTAAATTCCTCAATGATCgtgt                               >  1:251554/4‑139 (MQ=255)                                                                                             aaaaaGCTGCCCCTGAACAGGGCAGCTTTTTCA‑TTATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGAAATCCTCCGGCAGCGTAAATTCCTCAATGATCGTGTAGCGt                          <  8:292963/139‑1 (MQ=255)                                                                                                      ccccTGAACAGGGCAGCTTTTTCATTT‑TTTTTTCTGCAGAAGGCCCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGAAATCCTCCGGCAGCGTAAATTCCTCAATGATCGTGTAGCGTTCATTTGtt                 >  3:157704/1‑139 (MQ=255)                                                                                                      ccccTGAACAGGGCAGCTTTTTCA‑TTATTTTTTCTGCAGAAGGCCCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGAAATCCTCCGGCAGCGTAAATTCCTCAATGATCGTGTAGCGTTCATTTGtt                 >  5:149563/1‑139 (MQ=255)                                                                                                      ccccTGAACAGGGCAGCTTTTTCA‑TTATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGAAATCCTCCGGCAGCGTAAATTCCTCAATGATCGTGTAGCGTTCATTTGt                  <  8:155525/138‑1 (MQ=255)                                                                                                                gggCAGCTTTTTCA‑TTATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGAAATCCTCCGGCAGCGTAAATTCCTCAATGATCGTGTAGCGTTCATTTGTTTCTTTAAAgg       >  7:280148/1‑139 (MQ=255)                                                                                                                gggCAGCTTTTTCA‑TTATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGAAATCCTCCGGCAGCGTAAATTCCTCAATGATCGTGTAGCGTTCATTTGTTTCTTTAAAgg       >  8:278164/1‑139 (MQ=255)                                                                                                                 ggCAGCTTTTTCA‑TTATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGAAATCCTCCGGCAGCGTAAATTCCTCAATGATCGTGTAGCGTTCATTTGTTTCTTTAAAggc      >  4:78537/1‑139 (MQ=255)                                                                                                                 ggCAGCTTTTTCA‑TTATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGAAATCCTCCGGCAGCGTAAATTCCTCAATGATCGTGTAGCGTTCATTTGTTTCTTTAAAggc      >  4:201392/1‑139 (MQ=255)                                                                                                                   cAGCTTTTTCA‑TTATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGAAATCCTCCGGCAGCGTAAATTCTTCAATGATCGTGTAGCGTTCATTTGTTTCTTTAAAggcgg    >  1:181282/1‑139 (MQ=255)                                                                                                                    aGCTTTTTCA‑TTATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGAAATCCTCCGGCAGCGTAAATTCCTCAATGATCGTGTAGCGTTCATTTGTTTCTTTAAAggcggc   <  6:226623/139‑1 (MQ=255)                                                                                                                    aGCTTTTTCA‑TTATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGAAATCCTCCGGCAGCGTAAATTCCTCAATGATCGTGTAGCGTTCATTTGTTTCTTTAAAggcggc   <  7:12996/139‑1 (MQ=255)                                                                                                                    aGCTTTTTCA‑TTATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGAAATCCTCCGGCAGCGTAAATTCCTCAATGATCGTGTAGCGTTCATTTGTTTCTTTAAAggcggc   <  3:165149/139‑1 (MQ=255)                                                                                                                    aGCTTTTTCA‑TTATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCAGAAATCGTTTTGAAATCCTCCGGCAGCGTAAATTCCTCAATGATCGTGTAGCGTTCATTTGTTTCTTTAAAggcggc   <  5:55584/139‑1 (MQ=255)                                                                                                                     gCTTTTTCA‑TTATTTTTTCTTCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGAAATCCTCCGGCAGCGTAAATTCCTCAATGATCGTGTAGCGTTCATTTGTTTCTTTAAAGGCGGCa  <  4:207364/139‑1 (MQ=255)                                                                                                                     gCTTTTTCA‑TTATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGAAATCCTCCGGCAGCGTAAATTCCTCAATGATCGTGTAGCGTTCATTTGTTTCTTTAAAGGCGGCa  <  5:177952/139‑1 (MQ=255)                                                                                                                     gCTTTTTCA‑TTATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGAAATCCTCCGGCAGCGTAAATTCCTCAATGATCGTGTAGCGTTCATTTGTTTCTTTAAAGGCGGCa  <  7:278164/139‑1 (MQ=255)                                                                                                                     gCTTTTTCA‑TTATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGAAATCCTCCGGCAGCGTAAATTCCTCAATGATCGTGTAGCGTTCATTTGTTTCTTTAAAGGCGGCa  <  1:141060/139‑1 (MQ=255)                                                                                                                              |                                                                                                                                   TTTGACGAAATCAAACTTTCATCCGCATGGCATTAAAGTCCGTCTTGAAGATGGCCGCATCGGCCGCGACCAGCAGATCGTTTCTACATAAAAAAAAGCTGCCCCTGAACAGGGCAGCTTTTTCATTTATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGAAATCCTCCGGCAGCGTAAATTCCTCAATGATCGTGTAGCGTTCATTTGTTTCTTTAAAGGCGGCA  >  BS168_reference_genome/3935698‑3935953

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑