Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	BS168_reference_genome	3,099,285	T→C	7.1%	S55P (TCA→CCA)	msmF →	carbohydrate ABC transporter (permease)

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	BS168_reference_genome	3,099,285	0	T	C	7.1%	169.2 / 4.0	56	S55P (TCA→CCA)	msmF	carbohydrate ABC transporter (permease)
Reads supporting (aligned to +/- strand):  ref base T (33/19);  new base C (2/2);  total (35/21)
Fisher's exact test for biased strand distribution p-value = 6.26e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.34e-01

TGAAACAGGTTAAGCCAAAAAAGCAGTCCTCACTTTGGTGGATGTACATTCCTGCTTTGCTCTCCGTTCTGGTCTTTATGATTTACCCGTTTGTGAAAGGCACATTGATTACCTTTACAAACTGGAACGGATTTTCACAAGTCTACCAATGGGTTGGATTCGCGCAATATGAAAGGCTGTTTTCTGATCCTGATACTTGGCATATCTTAAAAAACACGCTGCATTACGGGCTTGGCAGCACCTTTTTTCAAAATGTGGTCGGGCTTCTG  >  BS168_reference_genome/3099151‑3099419                                                                                                                                       |                                                                                                                                       tgAAACAGGTTAAGCC‑AAAAAGCAGTCCTCACTTTGGTGGATGTACATTCCTGCTTTGCTCTCCGTTCTGGTCTTTATGATTTACCCGTTTGTGAAAGGCACATTGATTACCTTTACAAACTGGAACGGATTTTCACaa                                                                                                                                   <  5:313576/139‑1 (MQ=255)     aCAGGTTAAGCCAAAAAAGCAGTCCTCACTTTGGTGGATGTACATTCCTGCTTTGCTCTCCGTTCTGGTCTTTATGATTTACCCGTTTGTGAAAGGCACATTGATTACCTTTACAATCTGCAACGGATTTTCACAAGTc                                                                                                                                >  5:200657/1‑139 (MQ=255)            aaGCCAAAAAAGCAGTCCTCACTTTGGTGGATGTACATTCCTGCTTTGCTCTCCGTTCTGGTCTTTATGATTTACCCGTTTGTGAAAGGCACATTGATTACCTTTACAAACTGGAACGGATTTTCACAAGTCTACCAAt                                                                                                                         >  7:143697/1‑139 (MQ=255)             aGCCAAAAAAGCAGTCCTCACTTTGGTGGATGTACATTCCTGCTTTGCTCTCCGTTCTGGTCTTTATGATTTACCCGTTTGTGAAAGGCACATTGATTACCTTTACAAACTGGAACGGATTTCCACAAGTCTACCAATg                                                                                                                        >  7:113899/1‑139 (MQ=255)             aGCCAAAAAAGCAGTCCTCACTTTGGTGGATGTACATTCCTGCTTTGCTCTCCGTTCTGGTCTTTATGATTTACCCGTTTGTGAAAGGCACATTGATTACCTTTACAAACTGGAACGGATTTCCACAAGTCTACCAATg                                                                                                                        >  7:109992/1‑139 (MQ=255)                   aaaaGCAGTCCTCACTTTGGTGGATGTACATTCCTGCTTTGCTCTCCGTTCTGGTCTTTATGATTTACCCGTTTGTGAAAGGCAGATTGATTACCTTTACAACCTGGAACGGATTTTCACAAGTCTACCAATGGGTTg                                                                                                                   >  5:185294/1‑138 (MQ=255)                        cAGTCCTCACTTTGGTGGATGTACATTCCTGCTTTGCTCTCCGTTCTGGTCTTTATGATTTACCCGTTTGTGAAAGGCACATTGATTACCTTTACAAACTGGAACGGATTTTCACAAGTCTACCAATGGGTTGGATTcg                                                                                                             <  4:213735/139‑1 (MQ=255)                                aCTTTGGTGGATGTACATTCCTGCTTTGCTCTCCGTTCTGGTCTTTATGATTTACCCGTTTGTGAAAGGCACATTGATTACCTTTACAAACTGGAACGGATTTTCACAAGTCTACCAATGGGTTGGATTCGCGCAat                                                                                                       <  5:37459/137‑1 (MQ=255)                                       tggATGTACATTCCTGCTTTGCTCTCCGTTCTGGTCTTTATGATTTACCCGTTTGTGAAAGGCACATTGATTACCTTTACAAACTGGAACGGATTTTCACAAGTCTACCAAAGGGTTGGATTCGCGCAATATGAAAGGc                                                                                              >  8:8784/1‑139 (MQ=255)                                         gATGTACATTCCTGCTTTGCTCTCCGTTCTGGTCTTTATGATTTACCCGTTTGTGAAAGGCACATTGATTACCTTTACAAACTGGAACGGATTTTCACAAGTCTACCAATGGGTTGGATTCGCGCAATATGAAAGGCTg                                                                                            >  7:290348/1‑139 (MQ=255)                                          aTGTACATTCCTGCTTTGCTCTCCGTTCTGGTCTTTATGATTTACCCGTTTGTGAAAGGCACATTGATTACCTTTACAAACTGGAACGGATTTTCACAAGTCTACCAATGGGTTGGATTCGCGCAATATGAAAGGCTGt                                                                                           >  4:306738/1‑139 (MQ=255)                                            gTACATTCCTGCTTTGCTCTCCGTTCTGGTCTTTATGATTTACCCGTTTGTGAAAGGCACATTGATTACCTTTACAAACTGGAACGGATTTTCACAAGTCTACCAATGGGTTGGATTCGCGCAATATGAAAGGCTGttt                                                                                         >  8:187316/1‑139 (MQ=255)                                            gTACATTCCTGCTTTGCTCTCCGTTCTGGTCTTTATGATTTACCCGTTTGTGAAAGGCACATTGATTACCTTTACAAACTGGAACGGATTTTCACAAGTCTACCAATGGGTTGGATTCGCGCAATATGAAAGGCTGttt                                                                                         >  4:214784/1‑139 (MQ=255)                                            gTACATTCCTGCTTTGCTCTCCGTTCTGGTCTTTATGATTTACCCGTTTGTGAAAGGCACATTGATTACCTTTACAAACTGGAACGGATTTTCACAAGTCTACCAATGGGTTGGATTCGCGCAATATGAAAGGCTGttt                                                                                         >  6:220364/1‑139 (MQ=255)                                                    cTGCTTTGCTCTCCGTTCTGGTCTTTATGATTTACCCGTTTGTGAAAGGCACATTGATTACCTTTACAAACTGGAACGGATTTTCACAAGTCTACCAATGGGTTGGATTCGCGCAATATGAAAGGCTGtttt                                                                                        <  5:127989/132‑1 (MQ=255)                                                    cTGCTTTGCTCTCCGTTCTGGTCTTTATGATTTACCCGTTTGTGAAAGGCACATTGATTACCTTTACAAACTGGAACGGATTTTCACAAGTCTACCAATGGGTTGGATTCGCGCAATATGAAAGGCTGtttt                                                                                        >  6:127989/1‑132 (MQ=255)                                                     tGCTTTGCTCTCCGTTCTGGTCTTTATGATTTACCCGTTTGTGAAAGGCACATTGATTACCTTTACAAACTGGAACGGATTTTCACAAGTCTACCAATGGGTTGGATTCGCGCAATATGAAAGGCTGTTTTCTGATCCt                                                                                >  3:115320/1‑139 (MQ=255)                                                       cTTTGCTGTCGGTTCTGGTCTTTATGATTTTCCGGTTTGTGATCGGCACATTGATTACCTTTACAAACTGGAACGTTTTTTCACAAGTCTACAAATGGGTTGGATTCGCGCAATATGAAAGGAGGTTTTCTGATCCTg                                                                               <  1:210594/138‑1 (MQ=255)                                                            ctctCCGTTCTGGTCTTTATGATTTACCCGTTTGTGAAAGGCACATTGATTACCTTTACAAACTGGAACGGATTTTCACAAGTCTACCAATGGGTTGGATTCGCGCAATATGAAAGGCTGTTTTCt                                                                                      >  6:67504/1‑126 (MQ=255)                                                            ctctCCGTTCTGGTCTTTATGATTTACCCGTTTGTGAAAGGCACATTGATTACCTTTACAAACTGGAACGGATTTTCACAAGTCTACCAATGGGTTGGATTCGCGCAATATGAAAGGCTGTTTTCt                                                                                      <  5:67504/126‑1 (MQ=255)                                                                 cGTTCTGGTCTTTATGATTTACCCGTTTGTGAAAGGCACATTGATTACCTTTACAAACTGGAACGGATTTTCACAAGTCTACCAAAGGGTTGGATTCGCGCAATATGAAAGGCTGTTTTCTGATCCTGATACTTGGCa                                                                     >  7:125681/1‑138 (MQ=255)                                                                      tGGTCTTTATGATTTACCCGTTTGTGAAAGGCACATTGATTACCTTTACAAACTGGAACGGATTTTCACAAGTCTACCAATGGGTTGGATTCGCGCa                                                                                                         <  4:14064/97‑1 (MQ=255)                                                                      tGGTCTTTATGATTTACCCGTTTGTGAAAGGCACATTGATTACCTTTACAAACTGGAACGGATTTTCACAAGTCTACCAATGGGTTGGATTCGCGCa                                                                                                         >  3:14064/1‑97 (MQ=255)                                                                             taagATTTACCCGTTTGTGAAACGCACATTGATTACCTATACAAACTGGAACGGATTTTCACAAGTCTACCAAAGGCTTCGATTCGCGCAATATGTAAGGCTGTTTTCTGATCCTGATACTTGGCATATCATaaaaaa                                                         >  4:249139/4‑138 (MQ=255)                                                                             tATGATTTACCCGTTTGTGAAAGGCACATTGATTACCTTTACAAACTGGAACGGATTTTCACAAGTCTACCAATGGGTTGGATTCGCGCAATATGAAAGGCTGTTTTCTGATCCTGATACTTGGCATATCTTaaaaaa                                                         >  7:295621/1‑138 (MQ=255)                                                                             tATGATTTACCCGTTTGTGAAAGGCACATTGATTACCTTTACAAACTGGAACGGATTTTCACAAGTCTACCAATGGGTTGGATTCGCGCAATATGAAAGGCTGTTTTCTGATCCTGATACTTGGCATATCTTaaaaaa                                                         >  5:61247/1‑138 (MQ=255)                                                                             tATGATTTACCCGTTTGTGAAAGGCACATTGATTACCTTTACAAACTGGAACGGATTTTCACAAGTCTACCAATGGGTTGGATTCGCGCAATATGAAAGGCTGTTTTCTGATCCTGATACTTGGCATATCTTaaaaaa                                                         >  1:283920/1‑138 (MQ=255)                                                                                 aTTTACCCGTTTGTGAAAGGCACATTGATTACCTTTACAAACTGGAACGGATTTTCACAAGTCTACCAATGGGTTGGATTCGCGCAATATGAAAGGCTGTTTTCTGATCCTGATACTTGGCATATCTTAAAAAACACg                                                     <  8:295621/138‑1 (MQ=255)                                                                                 aTTTACCCGTTTGTGAAAGGCACATTGATTACCTTTACAAACTGGAACGGATTTTCACAAGTCTACCAATGGGTTGGATTCGCGCAATATGAAAGGCTGTTTTCTGATCCTGATACTTGGCATATCTTAAAAAACACg                                                     <  8:290348/138‑1 (MQ=255)                                                                                 aTTTACCCGTTTGTGAAAGGCACATTGATTACCTTTACAAACTGGAACGGATTTTCACAAGTCTACCAATGGGTTGGATTCGCGCAATATGAAAGGCTGTTTTCTGATCCTGATACTTGGCATATCTTAAAAAACACGc                                                    <  1:235996/139‑1 (MQ=255)                                                                                 aTTTACCCGTTTGTGAAAGGCACATTGATTACCTTTACAAACTGGAACGGATTTCCACAAGTCTACCACTGGGTTGGATTCGCGCAATATGAAAGGCTGTTTTCTGATCCTGATACTTGGCATATCTTAAAAAACACg                                                     <  8:109992/138‑1 (MQ=255)                                                                                 aTTTACCCGTTTGTGAAAGGCACATTGATTACCTTTACAAACTGGAACGGATTTCCACAAGTCTACCAATGGGTTGGATTCGCGCAATATGAAAGGCTGTTTTCTGATCCTGATACTTGGCATATCTTAAAAAACACg                                                     <  8:113899/138‑1 (MQ=255)                                                                                  tttACCCGTTTTTGAAAGGCACATTGATTACCTTTACAAACTGGAACGGATTTTCACAAGTCTACCAATGGGTTGGATTCGCGCAATATGAAAGGCTGTTTTCTGATCCTGATACTTGGCATATCTTAAAAAACACGCt                                                   <  6:17935/139‑1 (MQ=255)                                                                                  tttACCCGTTTGTGAAAGGCACATTGATTACCTTTACAAACTGGAACGGATTTTCACAAGTCTACCAATGGGTTGGATTCGCGCAATATGAAAGGCTGTTTTCTGATCCTGATACTTGGCATATCTTAAAAAACACGCt                                                   >  5:47475/1‑139 (MQ=255)                                                                                        cGTTTGTGAAAGGCACATTGATTACCTTTACAAACTGGAACGGATTTTCACAAGTCTACCAATGGGTTGGAATCGCGCAATATGAAAGGCTGTTTTCTGATCCTGATACTTGGCATATCTTAAAAAACACGCTGCATTa                                             <  8:131667/139‑1 (MQ=255)                                                                                          tttGTGAAAGGCACATTGATTACCTTTACAAACTGGAACGGATTTTCACAAGTCTACCAATGGGTTGGATTCGCGCAATATGAAAGGCTGTTTTCTGATCCTGATACTTGGCATATCTTAAAAAGCACGCTGCATTACg                                           >  1:152189/1‑139 (MQ=255)                                                                                          tttGTGAAAGGCACATTGATTACCTTTACAAACTGGAACGGATTTTCACAAGTCTACCAATGGGTTGGATTCGCGCAATATGAAAGGCTGTTTTCTGATCCTGATACTTGGCATATCTTAAAAAACACGCTGCATTACg                                           >  5:78346/1‑139 (MQ=255)                                                                                            tgtgAAAGGCACATTGATTACCTTTACAAACTGGAACGGATTTTCACAAGTCTACCAATGGGTTGGATTCGCGCAATATGAAAGGCTGTTTTCTGATCCTGATACTTGGCATATCTTAAAAAACACGc                                                    >  1:265358/1‑128 (MQ=255)                                                                                            tgtgAAAGGCACATTGATTACCTTTACAAACTGGAACGGATTTTCACAAGTCTACCAATGGGTTGGATTCGCGCAATATGAAAGGCTGTTTTCTGATCCTGATACTTGGCATATCTTAAAAAACACGc                                                    <  2:265358/128‑1 (MQ=255)                                                                                                   ggCACATTGATTACCTTTACAAACTGGAACGGATTTTCACAAGTCTACCAATGGGTTGGATTCGCGCAATATGAAAGGCTGTTTTCTGATCCTGATACTTGGCATATCTTAAAAAACACGCTGCATTACGGGCTTgg                                    >  5:297622/1‑137 (MQ=255)                                                                                                    gCACATTGATTACCTTTACAAACTGGAACGGATTTTCACAAGTCTACCAATGGGGTGGATTCGCGCAATATGAAAGGCTGTTTTCTGATCCTGATACTTGGCATATCTTAAAAAACACGCTGCATTACGGGCTTGgcag                                 <  3:214784/139‑1 (MQ=255)                                                                                                              tACCTTTACAAACTGGAACGGATTTTCACAAGTCTACCAATGGGTTGGATTCGCGCAATATGAAAGGCTGTTTTCTGATCCTGATACTCGGCATATCTTAAAAAACACGCTGCATTACGGGCTTGGCAGCACCtttttt                       >  4:64373/1‑139 (MQ=255)                                                                                                                    tACAAACTGGAACGGATTTTCACAAGTCTACCAATGGGTTGGATTCGCGCAATATGAAAGGCTGTTTTCt                                                                                      >  1:153124/1‑70 (MQ=255)                                                                                                                    tACAAACTGGAACGGATTTTCACAAGTCTACCAATGGGTTGGATTCGCGCAATATGAAAGGCTGTTTTCt                                                                                      <  2:153124/70‑1 (MQ=255)                                                                                                                    tACAAACTGGAACGGATTTTCACAAGTCTACCAATGGGTTGGATTCGCGCAATATGAAAGGCTGTTTTCTGATCCTGATACTTGGCATATCTTAAAAAACACGCTGCATTACGGGCTTGGCAGCACCTTTTTTCaaa                   <  1:289566/137‑1 (MQ=255)                                                                                                                    tACAAACTGGAACGGATTTTCACAAGTCTACCAATGGGTTGGATTCGCGCAATATGAAAGGCTGTTTTCTGATCCTGATACTTGGCATATCTTAAAAAACACGCTGCATTACGGGCTTGGCAGCACCTTTTTTCAAAAt                 >  1:1728/1‑139 (MQ=255)                                                                                                                    tACAAACTGGAACGGATTTTCACAAGTCTACCAATGGGTTGGATTCGCGCAATATGAAAGGCTGTTTTCTGATCCTGATACTTGGCATATCTTAAAAAACACGCTGCATTACGGGCTTGGCAGCACCTTTTTTCAAAAt                 >  8:94601/1‑139 (MQ=255)                                                                                                                         aCTTGATCGGATTTTCACAAGTCTAACAATGGGTTGGATTCGCGCAATATGAAAGGCTGTTTTCTGATCCTGATACTTGGCATATCTTAAAAAACACGCTGCATTACGGGCTTGGCAGCACCTTTTTTCAAAATGTGGt            <  8:125681/139‑1 (MQ=255)                                                                                                                           tGGAACGGATTTTCACAAGTCTACCAATGGGTTGGATTCGCGCa                                                                                                         <  7:225182/44‑1 (MQ=255)                                                                                                                           tGGAACGGATTTTCACAAGTCTACCAATGGGTTGGATTCGCGCa                                                                                                         >  8:225182/1‑44 (MQ=255)                                                                                                                           tGGAACGGATTTTCACAAGTCTACCAATGGGTTGGATTCGCGCAATATGAAAGGCTGTTTTCTGATCCTGATACTTGGCATATCTTAAAAAACACGCTGCATTACGGGCTTGGCAGCACCTTTTTTCAAAATGTGGTCg          >  4:226780/1‑139 (MQ=255)                                                                                                                           tGGAACGGATTTTCACAAGTCTACCAATGGGTTGGATTCGCGCAATATGAAAGGCTGTTTTCTGATCCTGATACTTGGCATATCTTAAAAAACACGCTGCATTACGGGCTTGGCAGCACCTTTTTTCAAAATGTGGTCg          >  2:84544/1‑139 (MQ=255)                                                                                                                           tGGAACGGATTTTCACAAGTCTACCAATGGGTTGGATTCGCGCAATATGAAAGGCTGTTTTCTGATCCTGATACTTGGCATATCTTAAAAAACACGCTGCATTACGGGCTTGGCAGCACCTTTTTTCAAAATGTGGTCg          >  8:184927/1‑139 (MQ=255)                                                                                                                           tGGAACGGATTTTCACAAGTCTACCAATGGGTTCGATTCGCGCAATATGAAAGACTGTTTTCTGATCCTGATACTTGGCATATCTTAAAAAACACGCTGCATAACGGGCTTGGCAGCACCTTTTTTCAAAATGTTGTCg          >  7:79668/1‑139 (MQ=255)                                                                                                                             gAACGGATTTTCACAAGTCTACCAATGGGTTGGATTCGCGCAATATGAAAGGCTGTTTTCTGATCCTGATACTTGGCATATCTTAAAAAACACGCTGCATTACGGGCTTGGCAGCACCTTTTTTCAAAATGTGGTCggg        <  3:306738/139‑1 (MQ=255)                                                                                                                                   aTTTTCACAAGTCTACCAATGGGTTGGATTCGCGCAATATGAAAGGCTGTTTTCTGATCCTGATACTTGGCATATCTTAAAAAACACGCTGCATTACGGGCTTGGCAGCACCTTTTTTCAAAATGTGGTCGGGCTTCTg  >  2:131438/1‑139 (MQ=255)                                                                                                                                       |                                                                                                                                       TGAAACAGGTTAAGCCAAAAAAGCAGTCCTCACTTTGGTGGATGTACATTCCTGCTTTGCTCTCCGTTCTGGTCTTTATGATTTACCCGTTTGTGAAAGGCACATTGATTACCTTTACAAACTGGAACGGATTTTCACAAGTCTACCAATGGGTTGGATTCGCGCAATATGAAAGGCTGTTTTCTGATCCTGATACTTGGCATATCTTAAAAAACACGCTGCATTACGGGCTTGGCAGCACCTTTTTTCAAAATGTGGTCGGGCTTCTG  >  BS168_reference_genome/3099151‑3099419

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑