Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP009974	1,920,768	Δ1 bp	intergenic (‑397/+158)	RPPX_08560 ← / ← RPPX_08565	16S ribosomal RNA/CoA‑transferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009974	1,920,768	0	C	.	97.8%	25.0 / ‑2.6	46	intergenic (‑397/+158)	RPPX_08560/RPPX_08565	16S ribosomal RNA/CoA‑transferase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base . (14/31);  minor base T (0/1);  total (14/32)
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

CTTGGAAGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTTGATCGTAGCCCTTACAGC‑‑A‑‑CCTTCCG‑‑AATCGTCTAACTCATTGAATCTCAAGGAGTTTGTCGTTCCGTTGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCTTTAATTTCAATAAC  >  CP009974/1920691‑1920868                                                                                    |                                                                                                     cTTGGAAGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑‑‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCgag                             >  1:6637093/1‑151 (MQ=2)  ttGGAAGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑‑‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCgaga                            <  2:5024406/151‑1 (MQ=2)  ttGGAAGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑‑‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCgaga                            <  1:3046133/151‑1 (MQ=2)   tGGAAGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑‑‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGagag                           >  1:4119053/1‑151 (MQ=2)   tGGAAGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑‑‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGagag                           <  2:1303239/151‑1 (MQ=2)    ggAAGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑‑‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAgg                          >  2:1995508/1‑151 (MQ=2)      aaGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑‑‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGc                        <  2:1388119/151‑1 (MQ=2)      aaGCGCTGTCAACCATCATCTCAACCGCTGTCGATCATTCGACCGTAGCCCCTCCAG‑‑‑‑‑‑CTTTCCGTTCACTACTTAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGc                        <  2:6839121/151‑1 (MQ=2)       aGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑‑‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCg                       >  2:2341582/1‑151 (MQ=2)       aGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑‑‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCg                       <  2:2874103/151‑1 (MQ=2)        gcgcTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGC‑‑TTTCCTTTC‑‑‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGt                      <  2:6916290/151‑1 (MQ=2)         cgcTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑‑‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTc                     <  1:378604/151‑1 (MQ=2)         cgcTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑‑‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTc                     >  1:5042906/1‑151 (MQ=2)         cgcTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑‑‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTc                     <  2:3333348/151‑1 (MQ=11)          gcTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑‑‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCa                    <  2:5607361/151‑1 (MQ=2)          gcTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑‑‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCa                    <  1:1907446/151‑1 (MQ=2)           cTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑‑‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCaa                   >  1:1123933/1‑151 (MQ=2)            tGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑‑‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAAc                  >  1:4591316/1‑151 (MQ=2)            tGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑‑‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAAc                  >  1:398788/1‑151 (MQ=2)            tGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑‑‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTAGGGCGCATTATAAGGGGATTCGAGAGGCCGTCAAc                  >  2:6976465/1‑151 (MQ=2)            tGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGC‑‑TTTCCTTTC‑‑‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAAc                  <  2:4593901/151‑1 (MQ=2)            tGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGC‑‑TTTCCTTTC‑‑‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAAc                  <  2:1509129/151‑1 (MQ=2)             gTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑‑‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCTTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAAcc                 >  2:4166387/1‑151 (MQ=2)             gTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑‑‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAAcc                 <  2:959855/151‑1 (MQ=2)             gTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑‑‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAAcc                 >  1:753115/1‑151 (MQ=2)              tCAACCATCCTCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑‑‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCt                <  2:334291/151‑1 (MQ=2)               cAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑‑‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCtt               <  1:139030/151‑1 (MQ=2)               cAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑‑‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCtt               <  2:3530059/151‑1 (MQ=2)               cAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑‑‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCtt               <  2:3530084/151‑1 (MQ=2)               cAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑‑‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCtt               <  2:3530100/151‑1 (MQ=2)               cAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑‑‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCtt               <  1:5295128/151‑1 (MQ=2)                aaCCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGC‑‑TTTCCTTTC‑‑‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCttt              <  2:1435900/151‑1 (MQ=2)                 aCCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑‑‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCTTTa             >  1:6537990/1‑151 (MQ=2)                  ccATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑‑‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCTTTaa            <  1:1968699/151‑1 (MQ=2)                   catcatCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑‑‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCTTTAAt           <  1:6156517/151‑1 (MQ=11)                   catcatCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑‑‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCTTTAAt           <  1:2222535/151‑1 (MQ=2)                    atcatcTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑‑‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCTTTAAtt          <  2:1170669/151‑1 (MQ=2)                     tcatcTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑‑‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCTTTAAttt         >  2:486889/1‑151 (MQ=2)                     tcatcTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑‑‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCTTTAAttt         <  1:2584786/151‑1 (MQ=2)                      catcTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑‑‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCCACCTTTAATTTc        <  2:3282127/151‑1 (MQ=2)                      catcTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑‑‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCTTTAATTTc        <  1:3454916/151‑1 (MQ=2)                      catcTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑‑‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCTTTAATTTc        >  1:5315539/1‑151 (MQ=2)                      catcTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑‑‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCTTTAATTTc        <  2:6943394/151‑1 (MQ=2)                       atcTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑‑‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCTTTAATTTCa       <  1:1993058/151‑1 (MQ=11)                           cAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑‑‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCTTTAATTTCAATaa   <  2:5330912/151‑1 (MQ=11)                            aaCCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑‑‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCTTTAATTTCAATAAc  <  1:7102878/151‑1 (MQ=11)                                                                                    |                                                                                                     CTTGGAAGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTTGATCGTAGCCCTTACAGC‑‑A‑‑CCTTCCG‑‑AATCGTCTAACTCATTGAATCTCAAGGAGTTTGTCGTTCCGTTGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCTTTAATTTCAATAAC  >  CP009974/1920691‑1920868

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑