Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,231,616	A→C	55.5%	S380S (TCT→TCG)	ptrB ←	protease II

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,231,616	0	A	C	55.5%	38.0 / 91.7	92	S380S (TCT→TCG)	ptrB	protease II
Reads supporting (aligned to +/- strand):  ref base A (10/31);  new base C (25/26);  total (35/57)
Fisher's exact test for biased strand distribution p-value = 1.85e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.14e-01

TACACGACGCTCACCGGTATCCATATCCAGTTCAAACAAAGTGTCTGGTGTAGTCATGGAAGAATAACCATAACGCAATCGCGCGGTTTCAGGTTCTGGATTGTAGGCAATCCAGGTCACA  >  minE/1231556‑1231676                                                             |                                                             tACACGACGCTCACCGGTATCCATATCCAGTTCAAACAAAGTGTCTGGTGTAGTCATGGAAGAATAAc                                                       <  1:1958744/68‑1 (MQ=255) tACACGACGCTCACCGGTATCCATATCCAGTTCAAACAAAGTGTCTGGTGTAGTCATGGAAGAATAAc                                                       <  1:1792476/68‑1 (MQ=255)   cacGACGCTCACCGGTATCCATATCCAGTTCAAACAAAGTGTCTGGTGTAGTCATGGAAGAAt                                                          <  1:3006602/63‑1 (MQ=255)   cacGACGCTCACCGGTATCCATATCCAGTTCAAACAAAGTGTCTGGTGTAGTCATGGAAGAATAACCAt                                                    <  1:2822346/69‑1 (MQ=255)   cacGACGCTCACCGGTATCCATATCCAGTTCAAACAAAGTGTCTGGTGTAGTCATGGAAGAATAACCAt                                                    <  1:1797883/69‑1 (MQ=255)   cacGACGCTCACCGGTATCCATATCCAGTTCAAACAAAGTGTCTGGTGTAGTCATGGAAGAATAACCAt                                                    <  1:2476746/69‑1 (MQ=255)   cacGACGCTCACCGGTATCCATATCCAGTTCAAACAAAGTGTCTGGTGTAGTCATGGAAGAATAACCAt                                                    <  1:2538510/69‑1 (MQ=255)   cacGACGCTCACCGGTATCCATATCCAGTTCAAACAAAGTGTCTGGTGTAGTCATGGAAGAATAACCAt                                                    <  1:1420457/69‑1 (MQ=255)   cacGACGCTCACCGGTATCCATATCCAGTTCAAACAAAGTGTCTGGTGTAGTCATGGAAGAATAACCAt                                                    <  1:2832489/69‑1 (MQ=255)   cacGACGCTCACCGGTATCCATATCCAGTTCAAACAAAGTGTCTGGTGTAGTCATGGAAGAATAACCAt                                                    <  1:2932690/69‑1 (MQ=255)   cacGACGCTCACCGGTATCCATATCCAGTTCAAACAAAGTGTCTGGTGTAGTCATGGAAGAATAACCAt                                                    <  1:1000790/69‑1 (MQ=255)   cacGACGCTCACCGGTATCCATATCCAGTTCAAACAAAGTGTCTGGTGTAGTCATGGAAGAATAACCAt                                                    <  1:409629/69‑1 (MQ=255)   cacGACGCTCACCGGTATCCATATCCAGTTCAAACAAAGTGTCTGGTCTAGTCATGGAAGAATAACCAt                                                    <  1:302048/69‑1 (MQ=255)        cgCTCACCTGTATCCATATCCAGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGc                                               <  1:245800/69‑1 (MQ=255)        cgCTCACCGGTATCCATATCCAGTTCAAACAAAGTGTCTGGTGTAGTCATGGAAGAATAACCATAACGc                                               <  1:694025/69‑1 (MQ=255)        cgCTCACCGGTATCCATATCCAGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGc                                               <  1:723876/69‑1 (MQ=255)        cgCTCACCGGTATCCATATCCAGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGc                                               <  1:2028650/69‑1 (MQ=255)        cgCTCACCGGTATCCATATCCAGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGc                                               <  1:2122444/69‑1 (MQ=255)        cgCTCACCGGTATCCATATCCAGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGc                                               <  1:2166342/69‑1 (MQ=255)        cgCTCACCGGTATCCATATCCAGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGc                                               <  1:2224888/69‑1 (MQ=255)        cgCTCACCGGTATCCATATCCAGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGc                                               <  1:2431351/69‑1 (MQ=255)        cgCTCACCGGTATCCATATCCAGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGc                                               <  1:818912/69‑1 (MQ=255)        cgCTCACCGGTATCCATATCCAGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGc                                               <  1:799241/69‑1 (MQ=255)        cgCTCACCGGTATCCATATCCAGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGc                                               <  1:735819/69‑1 (MQ=255)        cgCTCACCGGTATCCATATCCAGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGc                                               <  1:2572572/69‑1 (MQ=255)        cgCTCACCGGTATCCATATCCAGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGc                                               <  1:2655924/69‑1 (MQ=255)        cgCTCACCGGTATCCATATCCAGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGc                                               <  1:2810485/69‑1 (MQ=255)        cgCTCACCGGTATCCATATCCAGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGc                                               <  1:1030048/69‑1 (MQ=255)        cgCTCACCGGTATCCATATCCAGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGc                                               <  1:2897260/69‑1 (MQ=255)        cgCTCACCGGTATCCATATCCAGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGc                                               <  1:2897861/69‑1 (MQ=255)        cgCTCACCGGTATCCATATCCAGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGc                                               <  1:3073758/69‑1 (MQ=255)        cgCTCACCGGTATCCATATCCAGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGc                                               <  1:2965517/69‑1 (MQ=255)        cgCTCACCGGTATCCATATCCAGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGc                                               <  1:1940247/69‑1 (MQ=255)        cgCTCACCGGTATCCATATCCAGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGc                                               <  1:1720725/69‑1 (MQ=255)        cgCTCACCGGTATCCATATCCAGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGc                                               <  1:1807778/69‑1 (MQ=255)        cgCTCACCGGTATCCATATCCAGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGc                                               <  1:1173882/69‑1 (MQ=255)        cgCTCACCGGTATCCATATCCAGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGc                                               <  1:1392668/69‑1 (MQ=255)        cgCTCACCGGTATCCATATCCAGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGc                                               <  1:113628/69‑1 (MQ=255)        cgCTCACCGGTATCCATATCCAGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGc                                               <  1:1262928/69‑1 (MQ=255)                 gTATCCATATCCAGTTCAAACAAAGTATCTGGTGTGGTCATGGACGTATAACCATAACGc                                               <  1:656886/60‑1 (MQ=255)                     ccatatccaGTTCAAACAAAGTGTCTGGTGTAGTCATGGAAGAATAACCAt                                                    >  1:2844628/1‑51 (MQ=255)                     ccatatccaGTTCAAACAAAGTGTCTGGTGTAGTCATGGAAGAATAACCAt                                                    >  1:2430752/1‑51 (MQ=255)                     ccatatccaGTTCAAACAAAGTGTCTGGTGTAGTCATGGAAGAATAACCAt                                                    >  1:1252544/1‑51 (MQ=255)                     ccatatccaGTTCAAACAAAGTGTCTGGTGTAGTCATGGAAGAATAACCAt                                                    >  1:244202/1‑51 (MQ=255)                      catatccaGTTCAAACAAAGTGTCTGGTGTAGTCATGGAAGAATAACCATAACGCAATCGCGCGGTTTc                                 >  1:202803/1‑69 (MQ=255)                            caGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGCaa                                             >  1:3120904/1‑51 (MQ=255)                            caGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGCaa                                             >  1:1274960/1‑51 (MQ=255)                            caGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGCaa                                             >  1:2638253/1‑51 (MQ=255)                            caGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGCaa                                             >  1:2681148/1‑51 (MQ=255)                            caGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGCaa                                             >  1:2735063/1‑51 (MQ=255)                            caGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGCaa                                             >  1:2753325/1‑51 (MQ=255)                            caGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGCaa                                             >  1:610076/1‑51 (MQ=255)                            caGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGCaa                                             >  1:1439544/1‑51 (MQ=255)                            caGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGCaa                                             >  1:1239595/1‑51 (MQ=255)                            caGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGCaa                                             >  1:2844129/1‑51 (MQ=255)                            caGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGCaa                                             >  1:1281355/1‑51 (MQ=255)                            caGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGCaa                                             >  1:2581698/1‑51 (MQ=255)                            caGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGCaa                                             >  1:52244/1‑51 (MQ=255)                            caGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGCaa                                             >  1:1035623/1‑51 (MQ=255)                            caGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGCaa                                             >  1:1926184/1‑51 (MQ=255)                            caGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGCaa                                             >  1:2538617/1‑51 (MQ=255)                            caGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGCaa                                             >  1:2479384/1‑51 (MQ=255)                            caGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGCaa                                             >  1:2358148/1‑51 (MQ=255)                            caGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGCaa                                             >  1:1840200/1‑51 (MQ=255)                            caGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGCaa                                             >  1:1074232/1‑51 (MQ=255)                            caGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGCaa                                             >  1:2101085/1‑51 (MQ=255)                            caGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGCaa                                             >  1:2093629/1‑51 (MQ=255)                            caGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGCaa                                             >  1:1040066/1‑51 (MQ=255)                            caGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGCa                                              >  1:1767251/1‑50 (MQ=255)                            caGTTCAAACAAAGTATCTGGTGTGGTCATGGACGAATAACCATAACGCa                                              >  1:1285526/1‑50 (MQ=255)                                tCAAACAAAGTGTCTGGTGTAGTCATGGAAGAATAACCATAACGCAATCGCGCGGTTTCAGGTTCTgg                        >  1:2989885/1‑68 (MQ=255)                                 caaacaaaGTGTCTGGTGTAGTCATGGAAGAATAACCATAACGCAATCGCGCGGTTTCAGGTTCTGGAt                      >  1:921425/1‑69 (MQ=255)                                 caaacaaaGTGTCTGGTGTAGTCATGGAAGAATAACCATAACGCAATCGCGCGGTTTCAGGTTCTGGAt                      >  1:301609/1‑69 (MQ=255)                                 caaacaaaGTGTCTGGTGTAGTCATGGAAGAATAACCATAACGCAATCGCGCGGTTTCAGGTTCTGGAt                      <  1:1208183/69‑1 (MQ=255)                                 caaacaaaGTGTCTGGTGTAGTCATGGAAGAATAACCATAACGCAATCGCGCGGTTTCAGGTTCTGGAt                      >  1:1501107/1‑69 (MQ=255)                                 caaacaaaGTGTCTGGTGTAGTCATGGAAGAATAACCATAACGCAATCGCGCGGTTTCAGGTTCTGGAt                      <  1:1808860/69‑1 (MQ=255)                                 caaacaaaGTGTCTGGTGTAGTCATGGAAGAATAACCATAACGCAATCGCGCGGTTTCAGGTTCTGGAt                      >  1:2915366/1‑69 (MQ=255)                                 caaacaaaGTGTCTGGTGTAGTCATGGAAGAATAACCATAACGCAATCGCGCGGTTTCAGGTTCTGGAt                      <  1:2620113/69‑1 (MQ=255)                                  aaacaaaGTGTCTGGTGTAGTCATGGAAGAATAACCATAACGCAATCGCGCGGTTTCAGGTTCTGGAt                      <  1:532123/68‑1 (MQ=255)                                  aaacaaaGTGTCTGGTGTAGTCATGGAAGAATAACCATAACGCAATCGCGCGGTTTCAGGTTCTGGAt                      <  1:308751/68‑1 (MQ=255)                                     caaaGTGTCTGGTGTAGTCATGGAAGAATAACCATAACGCAATCGCGCGGTTTCAGGTTCTGGATTGTa                  <  1:1207647/69‑1 (MQ=255)                                     caaaGTGTCTGGTGTAGTCATGGAAGAATAACCATAACGCAATCGCGCGGTTTCAGGTTCTGGATTGTa                  <  1:1933873/69‑1 (MQ=255)                                         gtgtCTGGTGTAGTCATGGAAGAATAACCATAACGc                                               <  1:2417478/36‑1 (MQ=255)                                            tCTGGTGTAGTCATGGAAGAATAACCATAACGCAATCGCGCGGTTTCAGGTTCTGGATTGTAGGCAATc           <  1:1565096/69‑1 (MQ=255)                                                   tAGTCATGGAAGAATAACCATAACGCAATCGCGCGGTTTc                                 <  1:2551362/40‑1 (MQ=255)                                                   tAGTCATGGAAGAATAACCATAACGCAATCGCGCGGTTTCAGGTTCTGGATTGTAGGCAATCCAGGTca    <  1:430626/69‑1 (MQ=255)                                                   tAGTCATGGAAGAATAACCATAACGCAATCGCGCGGTTTCAGGTTCTGGATTGTAGGCAATCCAGGTca    <  1:1681507/69‑1 (MQ=255)                                                   tAGTCATGGAAGAATAACCATAACGCAATCGCGCGGTTTCAGGTTCTGGATTGTAGGCAATCCAGGTca    <  1:1990840/69‑1 (MQ=255)                                                        aTGGAAGAATAACCATAACGCAATCGCGCGGTTTCAGGTTCTGGATTGTAGGCAATCCAGGTcaca  <  1:2622145/66‑1 (MQ=255)                                                        aTGGAAGAATAACCATAACGCAATCGCGCGGTTTCAGGTTCTGGATTGTAGGCAATCCAGGTcaca  <  1:1213949/66‑1 (MQ=255)                                                        aTGGAAGAATAACCATAACGCAATCGCGCGGTTTCAGGTTCTGGATTGTAGGCAATCCAGGTcaca  <  1:1863792/66‑1 (MQ=255)                                                        aTGGAAGAATAACCATAACGCAATCGCGCGGTTTCAGGTTCTGGATTGTAGGCAATCCAGGTcaca  <  1:2029990/66‑1 (MQ=255)                                                             |                                                             TACACGACGCTCACCGGTATCCATATCCAGTTCAAACAAAGTGTCTGGTGTAGTCATGGAAGAATAACCATAACGCAATCGCGCGGTTTCAGGTTCTGGATTGTAGGCAATCCAGGTCACA  >  minE/1231556‑1231676

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