Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,277,950	T→C	noncoding (117/140 nt)	ryjA ←	small RNA RyjA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,277,950	0	T	C	98.0%	163.9 / ‑4.2	49	noncoding (117/140 nt)	ryjA	small RNA RyjA
Reads supporting (aligned to +/- strand):  ref base T (1/0);  new base C (24/24);  total (25/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.74e-01

TGGACGGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCTTTAGTTTGTTTTCCGGTCTTTGTCTTTCTCTCTATCCCGCTGGTACACAGGAGGGTTTCCCCCGACGTCAACACACCTCATTCGAGCACGTGGTGGAGGTTCCGGTTGGTGTTGATGCTTTAATTGTATGTCACCG  >  NC_000913/4277815‑4278086                                                                                                                                        |                                                                                                                                         tGGACGGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCCTTAg                                                                                                                                      >  1:671206/1‑140 (MQ=255)   gACGGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCCTTAgtt                                                                                                                                    >  2:577712/1‑140 (MQ=255)         tGTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCCTTAGTTTGtttt                                                                                                                              <  2:434957/140‑1 (MQ=255)          gTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCCTTAGTTTGTTTTc                                                                                                                             <  2:759020/140‑1 (MQ=255)              tGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCCTTAGTTTGTTTTCCGgt                                                                                                                         >  2:610366/1‑140 (MQ=255)                  tgtgGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAATGGCGCCTTAGTTTGTTTTCCGgtcttt                                                                                                                     <  2:95512/140‑1 (MQ=255)                  tgtgGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACACGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCCTTAGTTTGTTTTCCGgtct                                                                                                                       >  2:418037/1‑138 (MQ=255)                  tgtgGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACACGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCCTTAGTTTGTTTTCCGgtct                                                                                                                       <  1:418037/138‑1 (MQ=255)                   gtgGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCCTTAGTTTGTTTTCCGgtctttg                                                                                                                    >  1:59199/1‑140 (MQ=255)                     ggCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCCTTAGTTTGTTTTCCGgtctttgtc                                                                                                                  <  1:164138/140‑1 (MQ=255)                      gCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCCTTAGTTTGTTTTcc                                                                                                                            <  2:613943/129‑1 (MQ=255)                      gCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCCTTAGTTTGTTTTcc                                                                                                                            >  1:613943/1‑129 (MQ=255)                      gCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCCTTAGTTTGTTTTCCGgtctttgtct                                                                                                                 <  1:466604/140‑1 (MQ=255)                       cTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCCTTAGTTTGTTTTCCGgtctttgtctt                                                                                                                <  2:830233/140‑1 (MQ=255)                                gcgcAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCCTTAGTTTGTTTTCCGGTCTTTGTCTTTCTCTCTAt                                                                                                       <  2:671206/140‑1 (MQ=255)                                  gcAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCCTTAGTTTGTTTTCCGGTCTTTGTCTTTCTCTCTATcc                                                                                                     <  2:59199/140‑1 (MQ=255)                                        aTTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCCTTAGTTTGTTTTCCGGTCTTTGTCTTTCTCTCTATcc                                                                                                     <  2:801326/134‑1 (MQ=255)                                        aTTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCCTTAGTTTGTTTTCCGGTCTTTGTCTTTCTCTCTATcc                                                                                                     >  1:801326/1‑134 (MQ=255)                                        aTTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCCTTAGTTTGTTTTCCGGTCTTTGTCTTTCTCTCTATCCCGc                                                                                                  >  2:659809/1‑137 (MQ=255)                                        aTTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCCTTAGTTTGTTTTCCGGTCTTTGTCTTTCTCTCTATCCCGc                                                                                                  <  1:659809/137‑1 (MQ=255)                                        aTTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCCTTAGTTTGTTTTCCGGTCTTTGTCTTTCTCTCTATCCCGCTgg                                                                                               >  2:435021/1‑140 (MQ=255)                                                ttGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCCTTAGTTTGTTTTCCGGTCTTTGTCTTTCTCTCTATCCCGCTGGTACACagg                                                                                       >  2:662619/1‑140 (MQ=255)                                                ttGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCCTTAGTTTGTTTTCCGGTCTTTGTCTTTCTCTCTATCCCGCTGGTACACagg                                                                                       >  2:719673/1‑140 (MQ=255)                                                          cGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCCTTAGTTTGTTTTCCGGTCTTTGTCTTTCTCTCTATCCCGCTGGTACACAGGAGGGTTTccc                                                                             <  1:435021/140‑1 (MQ=255)                                                             gCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCCTTAGTTTGTTTTCCGGTCTTTGTCTTTCTCTCTATCCCGCTGGTACACAGGAGGGTTTCCCCCg                                                                          >  2:73748/1‑140 (MQ=255)                                                                  cGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCCTTAGTTTGTTTTCCGGTCTTTGTCTTTCTTTCTATCCCGCTGGTACACAGGAGGGTTTCCCCCGACGTc                                                                     >  2:277991/1‑140 (MQ=255)                                                                  cGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCCTTAGTTTGTTTTCCGGTCTTTGTCTTTCTCTCTATCCCGCTGGTACACAGGAGGGTTTCCCCCGACGTc                                                                     >  1:128043/1‑140 (MQ=255)                                                                    cTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCCTTAGTTTGTTTTCCGGTCTTTGTCTTTCTCTCTATCCCGCTGGTACACAGGAGGGTTTCCCCCGACGTCaa                                                                   >  1:657889/1‑140 (MQ=255)                                                                        ggAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCCTTAGTTTGTTTTCCGGTCTTTGTCTTTCTCTCTATCCCGCTGGTACACAGGAGGGTTTCCCCCGACGTCAacaca                                                               <  1:113087/140‑1 (MQ=255)                                                                             agaagGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCCTTAGTTTGTTTTCCGGTCTTTGTCTTTCTCTCTATCCCGCTGGTACACAGGAGGGTTTCCCCCGACGTCAACACACCTCa                                                          <  2:726443/140‑1 (MQ=255)                                                                                 ggTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCCTTAGTTTGTTTTCCGGTCTTTGTCTTTCTCTCTATCCCGCTGGTACACAGGAGGGTTTCCCCCGACGTCaa                                                                   <  2:432499/127‑1 (MQ=255)                                                                                 ggTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCCTTAGTTTGTTTTCCGGTCTTTGTCTTTCTCTCTATCCCGCTGGTACACAGGAGGGTTTCCCCCGACGTCaa                                                                   >  1:432499/1‑127 (MQ=255)                                                                                    aCCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCCTTAGTTTGTTTTCCGGTCTTTGTCTTTCTCTCTATCCCGCTGGTACACAGGAGGGTTTCCCCCGACGTCAACACACCTCATTCGAGc                                                   >  2:681027/1‑140 (MQ=255)                                                                                    aCCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCCTTAGTTTGTTTTCCGGTCTTTGTCTTTCTCTCTATCCCGCTGGTACACAGGAGGGTTTCCCCCGACGTCAACACACCTCATTCGAGc                                                   <  1:562118/140‑1 (MQ=255)                                                                                           cACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCCTTAGTTTGTTTTCCGGTCTTTGTCTTTCTCTCTATCCCGCTGGTACACAGGAGGGTTTCCCCCGACGTCAACACACCTCATTCGAGCACgtggt                                            <  1:719673/140‑1 (MQ=255)                                                                                            aCGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCCTTAGTTTGTTTTCCGGTCTTTGTCTTTCTCTCTATCCCGCTGGTACACAGGAGGGTTTCCCCCGACGTCAACACACCTCATTCGAGCACgtggtg                                           >  1:619871/1‑140 (MQ=255)                                                                                             cGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCCTTAGTTTGTTTTCCGGTCTTTGTCTTTCTCTCTATCCCGCTGGTACACAGGAGGGTTTCCCCCGACGTCAACACACCTCATTCGAGCACGtggtgg                                          <  1:430294/140‑1 (MQ=255)                                                                                                 tGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCCTTAGTTTGTTTTCCGGTCTTTGTCTTTCTCTCTATCCCGCTGGTACACAGGAGGGTTTCCCCCGACGTCAACACACCTCATTCGAGCACGTGGTGGAGGt                                      <  1:681027/140‑1 (MQ=255)                                                                                                        aGATGAACAAAACTAAAGCGCCACAAGGGCGCCTTAGTTTGTTTTCCGGTCTTTGTCTTTCTCTCTATCCCGCTGGTACACAGGAGGGTTTCCCCCGACGTCAACACACCTCATTCGAGCACGTGGTGGAGGTTCCGGtt                               >  2:737232/1‑140 (MQ=255)                                                                                                        aGATGAACAAAACTAAAGCGCCACAAGGGCGCCTTAGTTTGTTTTCCGGTCTTTGTCTTTCTCTCTATCCCGCTGGTACACAGGAGGGTTTCCCCCGACGTCAACACACCTCATTCGAGCACGTGGTGGAGGTTCCGGt                                <  1:666478/139‑1 (MQ=255)                                                                                                        aGATGAACAAAACTAAAGCGCCACAAGGGCGCCTTAGTTTGTTTTCCGGTCTTTGTCTTTCTCTCTATCCCGCTGGTACACAGGAGGGTTTCCCCCGACGTCAACACACCTCATTCGAGCACGTGGTGGAGGTTCCGGt                                >  2:666478/1‑139 (MQ=255)                                                                                                            gAACAAAACTAAAGCGCCACAAGGGCGCCTTAGTTTGTTTTCCGGTCTTTGTCTTTCTCTCTATCCCGCTGGTACACAGGAGGGTTTCCCCCGACGTCAACACACCTCATTCGAGCACGTGGTGGAGGTTCCGGTTGgtg                           >  1:569304/1‑140 (MQ=255)                                                                                                                aaaaCTAAAGCGCCACAAGGGCGCCTTAGTTTGTTTTCCGGTCTTTGTCTTTCTCTCTATCCCGCTGGTACACAGGAGGGTTTCCCCCGACGTCAACACACCTCATTCGAGCACGTGGTGGAGGTTCCGGTTGGTGTTGa                       <  1:737232/140‑1 (MQ=255)                                                                                                                    cTAAAGCGCCACAAGGGCGCCTTAGTTTGTTTTCCGGTCTTTGTCTTTCTCTCTATCCCGCTGGTACACAGGAGGGTTTCCCCCGACGTCAACACACCTCATTCGAGCACGTGGTGGAGGTTCCGGTTGGTGTTGATGCt                   <  2:619871/140‑1 (MQ=255)                                                                                                                      aaaGCGCCACAAGGGCGCCTTAGTTTGTTTTCCGGTCTTTGTCTTTCTCTCTATCCCGCTGGTACACAGTAGGGTTTCCCCCGACGTCAACACACCTCATTCGAGCACGTGGTGGAGGTTCCGGTTGGTGTTGATGCttt                 >  2:520977/1‑140 (MQ=255)                                                                                                                        aGCGCCACAAGGGCGCCTTAGTTTGTTTTCTGGTCTTTGTCTTTCTCTCTATCCCGCTGGTACACAGGAGGGTTTCCCCCGACGTCAACACACCTCATTCGAGCACGTGGTGGAGGTTCCGGTTGGTGTTGATGCTTTaa               <  1:520977/140‑1 (MQ=255)                                                                                                                          cgcCACAAGGGCGCCTTAGTTTGTTTTCCGGTCTTTGTCTTTCTCTCTATCCCGCTGGTACACAGGAGGGTTTCCCCCGACGTCAACACACCTCATTCGAGCACGTGGTGGAGGTTCCGGTTGGTGTTGATGCTTTAAtt             >  1:445365/1‑140 (MQ=255)                                                                                                                            ccACAAGGGCGCCTTAGTTTGTTTTCCGGTCTTTGTCTTTCTCTCTATCCCGCTGGTACACAGGAGGGTTTCCCCCGACGTCAACACACCTGATTCGAGCACGTCGAGTAGGTTCCGTTTGGCGTTGATGCTTTAATTGt           >  2:363900/1‑140 (MQ=255)                                                                                                                                     cgcTTTAGTTTGTTTTCCGGTCTTTGTCTTTCTCTCTATCCCGCTGGTACACAGGAGGGTTTCCCCCGACGTCAACACACCTCATTCGAGCACGTGGTGGAGTTTCCGGTAGGTTTTCATGCTTCAATTGTATGTCACCg  >  1:292733/1‑140 (MQ=255)                                                                                                                                        |                                                                                                                                         TGGACGGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCTTTAGTTTGTTTTCCGGTCTTTGTCTTTCTCTCTATCCCGCTGGTACACAGGAGGGTTTCCCCCGACGTCAACACACCTCATTCGAGCACGTGGTGGAGGTTCCGGTTGGTGTTGATGCTTTAATTGTATGTCACCG  >  NC_000913/4277815‑4278086

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑