Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,163,377	0	G	T	44.7%	61.9 / 24.4	47	E40* (GAA→TAA)	thiK	thiamine kinase
Reads supporting (aligned to +/- strand):  ref base G (3/23);  new base T (21/0);  total (24/23)
Fisher's exact test for biased strand distribution p-value = 1.81e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGGGCGAAATTATCTGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAG‑TTTTCTCATTGAACAT‑CAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATG‑CGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATATCTCCGTGACTGGATGGT  >  NC_000913/1163233‑1163522                                                                                                                                                  |                                                                                                                                                    cGGGCGAAATTATCTGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAG‑TTTTCTCATTGAACAT‑c                                                                                                                                              <  2:552460/151‑1 (MQ=255)        aaTTATCTGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAG‑TTTTCTCATTGAACAT‑CAGGGCCa                                                                                                                                       <  2:141384/151‑1 (MQ=255)               tGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAG‑GTTTTTTCTTTTACAT‑CAGGGGCAGAGgttt                                                                                                                                >  2:529154/1‑151 (MQ=255)                ggTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAG‑TTTTCTCATTGAACAT‑CAGGGCCAGCGttt                                                                                                                                 <  1:757282/149‑1 (MQ=255)                  tCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGGG‑TTTTTTTTTTTAACAT‑CAAGGGCAGCGTtttttt                                                                                                                             >  2:371121/1‑151 (MQ=255)                       tAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGGG‑TTTTTTTCTTTTAAAT‑CAAGGCCAGCGGTttgtt                                                                                                                             >  2:643138/1‑146 (MQ=255)                        aaaGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGGG‑GTTTTTTTTTTTACAT‑CAAGGCCAGCGGTttgtt                                                                                                                             >  2:97430/1‑145 (MQ=255)                        aaaGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAG‑TTTTCTCATTGAACAT‑CAGGGCCAGCGTTTTGTTGTGCg                                                                                                                        <  2:669820/150‑1 (MQ=255)                        aaaGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAG‑GTTTTTCCTTTAAAAT‑CAAGGCCACCGGtttttttt                                                                                                                           >  2:830630/1‑145 (MQ=255)                          aGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAG‑TTTTCTCATTGAACAT‑CAGGGCCAGCGTTTTGTTGTGCGTCa                                                                                                                     <  2:112681/151‑1 (MQ=255)                            gTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAG‑TTTTCTCATTGAACAT‑CAGGGCCAGCGTTTTGTTGTGCGTCAGc                                                                                                                   <  1:140476/151‑1 (MQ=255)                                 gTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGGGCTTTTCTATTTTAAAAC‑CAGGG‑CAGCGTTTTTTTGTGCGtgcttc                                                                                                                  >  1:111199/1‑142 (MQ=255)                                 gTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAG‑TTTTCTCATTGAACAT‑CAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCAc                                                                                                              <  2:438006/151‑1 (MQ=255)                                 gTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAG‑GTTTTTCATTTAACAT‑CAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCAc                                                                                                              >  1:402688/1‑151 (MQ=255)                                  tttCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAG‑GTTTTTTCTTTAACAA‑CCAGGCCAGCGTTTTTTTGTGTGGTAGCCCCAc                                                                                                              >  1:899057/1‑150 (MQ=255)                                   ttCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAG‑TTTTCTCATTGAACAT‑CAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACg                                                                                                             <  1:78514/150‑1 (MQ=255)                                    tCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGGG‑GTTTTTTTTTTTAAAT‑CAAGGGCCGCGGTTTTTtgtgtggccgcccccc                                                                                                              >  2:315153/1‑136 (MQ=255)                                     cGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAG‑TTTTCTCATTGAACAT‑CAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGAt                                                                                                           <  1:74028/150‑1 (MQ=255)                                        agcaATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGGG‑GTTTTTCCTTTACAAT‑TACGGCCAGAGGTTTGTTGGTCGCCAGCCGCCCGATcc                                                                                                         >  2:688921/1‑149 (MQ=255)                                         gcaATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGGG‑GTTTTTCATTTAAAAT‑CAAGGCCAGCGGTTTTTTTTGTGTCAGccccccggacctgt                                                                                                      >  2:705763/1‑139 (MQ=255)                                            ataatCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAG‑TTTTCTCATTGAACAT‑CAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATg‑c                                                                                                  <  1:639713/151‑1 (MQ=255)                                                   cATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGGG‑GTTTTTCATTTAACAT‑CAGAGCCAGCGGTTTTTTGTGCGTCAGCCGCACCATCCTGATg‑c                                                                                                  >  2:268404/1‑144 (MQ=255)                                                   cATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAG‑TTTTCTCATTGAACAT‑CAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATG‑CGCCGCAg                                                                                           <  1:628885/151‑1 (MQ=255)                                                    aTCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGGG‑GTTTTTCATTTAAAATACAGGGCC‑GCGGTTTTTTGTGCGGCAGCCGCCCGGCCctgctg                                                                                                    >  1:349032/1‑142 (MQ=255)                                                      cACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAG‑TTTTCTCATTGAACAT‑CAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATG‑CGCCGCAGTc                                                                                         <  2:678945/150‑1 (MQ=255)                                                         gcgcgACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAG‑TTTTCTCATTGAACAT‑CAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATG‑CGCCGCAGTCcgcg                                                                                     <  1:738245/151‑1 (MQ=255)                                                          cgcgACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAG‑TTTTCTCATTGAACAT‑CAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATG‑CGCCGCAGTCCGCGt                                                                                    <  1:546588/151‑1 (MQ=255)                                                            cgacgaATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGGG‑GTTTTTCATTTAACAT‑CAAGGGCAGCGGTTTTTTTTGGGTTCGCCGCCCCACCCTGCTG‑CGCCCCCGTCcgcggt                                                                                   >  1:121110/1‑148 (MQ=255)                                                              acgaATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAG‑TTTTCTCATTGAACAT‑CAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATG‑CGCCGCAGTCCGCGTTCtt                                                                                <  2:519215/151‑1 (MQ=255)                                                                   ttGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGGG‑GTTTTTTCTTGAACAT‑CACGGCCCGCGGTTTTTTGTGCGTCAGCCGGCCGGTTCTCATGCCGCCCCGGTCCGc‑ttctttggc                                                                            >  2:781002/1‑146 (MQ=255)                                                                     gCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAG‑GTTTTTCTTTTTACAT‑CACGGCCAGCGGTTTTTTTTGCGTCTGCCGCCCGAACCTCATG‑CCCCCCAGTCCCCGCTCTTGTGcc                                                                           >  1:841633/1‑149 (MQ=255)                                                                           gcgcTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAG‑GTTTTTTTTTTTACAT‑CAAGGCCAGCGGTTTTTTGTGCGGCAACCGCCCGATCCCTAAG‑CGCCGCCGGCCGCGGTCTTGCGCCCGTATCgg                                                                   >  1:132606/1‑151 (MQ=255)                                                                              cTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGGG‑TTTTTTCTTTTAAAAC‑CAAGGCCACCGTTTTTTTGTGGGTCGGCCGCGCGACCCTTCTG‑CTCCCCAGTCCCCGGTCttttccccggaacggg                                                                  >  2:50830/1‑135 (MQ=255)                                                                               tttttCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGGG‑GTTTTTCTTTGAATAA‑CAAGGCCACCGCTTTTTTTTGCGTTAGCCGCACGGTCCCGGTG‑GGCCGCAGTCCCCGGTCTTGCGccccgtttggggct                                                               >  2:840801/1‑139 (MQ=255)                                                                                 tttCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAG‑TTTTCTCATTGAACAT‑CAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATG‑CGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCttt                                                              <  2:312334/150‑1 (MQ=255)                                                                                                    gTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAG‑TTTTCTCATTGAACAT‑CAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATG‑CGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCgcatgca                                          <  1:455332/151‑1 (MQ=255)                                                                                                           cgTTTAATAGTGGGCTTAGTGGCGGGGG‑GTTTTTCCTTTTACAT‑CAAGGGCAGCGGTTTGTTGTGCGTCAGCCGCCCCATCCTGATG‑CGCCCCCGGCCCCGTTCTTTCGCCAGGATCGGGCTTTTTTACAACCACCCCCCCGCATTTCAcc                                   >  2:85860/1‑151 (MQ=255)                                                                                                             tttAATAGTGGGCTTAGTGGCGGGGG‑GTTTTTTATTTAAAAT‑CAAGGGCCGCGTTTTTTTTTGGGTCTGCCGCACGATCCTGATG‑CGCCGCCGGGCGCGTTTTTTTGCCCGGATTGGGGGTTTTTACAAACACCCGCCCGCAttttacc                                   >  2:171065/1‑144 (MQ=255)                                                                                                                 aTAGTGGGCTTAGTGGCGGGGG‑GTTTTTCTTTTTAAAT‑CAAGGGCAGCGGTTTTTTTTGGGGGCGCCGCACGATCCTCATG‑GGCCGCCGGCCGCGTTTTTTCGCCCGGATAGGGGGTTTTTACAAACAACCCCATGCATTTCAcc                                   >  2:969345/1‑145 (MQ=255)                                                                                                                 aTAGTGGGCTTAGTGGCGGGAG‑TTTTCTCATTGAACAT‑CAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATG‑CGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGcc                             <  1:623451/151‑1 (MQ=255)                                                                                                                 aTAGTGGGCTTAGTGGCGGGAG‑TTTTCTCATTGAACAT‑CAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATG‑CGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGcc                             <  2:262203/151‑1 (MQ=255)                                                                                                                  tAGTGGGCTTAGTGGCGGGGG‑GTTTTTCCTTTAACAA‑CAGGGCCCGCGGTTTTTTGTGGGTCAGCCGCACGATCCTGATG‑CGCCGCCGGCCGCGTTTTTTCGCCCGGATCGGGGTTTTTCACAACCACCCCCCCGCATTTCACCCAAGcc                             >  1:443935/1‑150 (MQ=255)                                                                                                                   aGTGGGCTTAGTGGCGGGAG‑TTTTCTCATTGAACAT‑CAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATG‑CGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGc                           <  1:265592/151‑1 (MQ=255)                                                                                                                        gCTTAGTGGCGGGAG‑TTTTCTCATTGAACAT‑CAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATG‑CGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTta                      <  1:881224/151‑1 (MQ=255)                                                                                                                               ggCGGGAG‑TTTTCTCATTGAACAT‑CAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATG‑CGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATATCTcc               <  2:480336/151‑1 (MQ=255)                                                                                                                                        ttttCTCATTGAACAT‑CAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATG‑CGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATATCTCCGTGACTgg       >  2:516490/1‑151 (MQ=255)                                                                                                                                              cATTGAACAT‑CAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATG‑CGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATATCTCCGTGACTGGATGGt  <  1:862294/150‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                                    CGGGCGAAATTATCTGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAG‑TTTTCTCATTGAACAT‑CAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATG‑CGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATATCTCCGTGACTGGATGGT  >  NC_000913/1163233‑1163522

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑