Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 1,064,082 G→T 19.0% A136E (GCA→GAA)  USA300HOU_1000 ← LytR family transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,064,0820GT19.0% 39.1 / 4.4 21A136E (GCA→GAA) USA300HOU_1000LytR family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (12/5);  new base T (2/2);  total (14/7)
Fisher's exact test for biased strand distribution p-value = 5.74e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.69e-01

GTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATGCTTTCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTA  >  CP000730/1063944‑1064210
                                                                                                                                          |                                                                                                                                 
gtgtTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATGCTTTCATATTGACTCTCACATAATAATCAACAGATACATTCATGGTAGCTTCTACCGAATCCATTGCg                                                                                                                                >  1:66951/1‑141 (MQ=255)
 tgtTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATGCTTTCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTTCgg                                                                                                                               <  2:275472/141‑1 (MQ=255)
 tgtTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATGCTTTCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCgg                                                                                                                               >  1:135665/1‑141 (MQ=255)
                aGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATGCTTTCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCat                                                                                                                >  1:244807/1‑141 (MQ=255)
                                atAGTATATGCCACCACGCTCATTTACATCCTCGACAAATGCTTTCATATTGACTCTCACATAATAATCACCAGGTACAATCAAGGTAGCCTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGt                                                                                                <  1:167/141‑1 (MQ=255)
                                       atGCCACCAAGCTCATTTACAGCCTCGACAATTGCTTTCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTa                                                                                         <  2:281282/141‑1 (MQ=255)
                                        tGCCACCAAGCTCATTTACAGCCTCGACAAATGCTTTCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCAAGTGCATGGGTCACCTTAt                                                                                        >  2:32476/1‑141 (MQ=255)
                                                   tCATTTACAGCCTCGACAAATGCTTTCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTTCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCGTAATAGCCa                                                                             >  1:246938/1‑141 (MQ=255)
                                                     aTTTACAGCCTCGACAAATGCTTTCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCCTGGGCAATCTTTTCGTAATAGCCAAc                                                                           <  2:334377/141‑1 (MQ=255)
                                                            gCCTCGACAAATGCTTTCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCGTAATAGCCAACTTTAGGa                                                                    <  1:5163/141‑1 (MQ=255)
                                                                                   gACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTgg                                             >  2:179794/1‑141 (MQ=255)
                                                                                    aCTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGa                                            >  2:298752/1‑141 (MQ=255)
                                                                                       ctcACGTAATAATCAACGGGTACATTCATGGTAGCTACTACCGAATAAACTGTCGTGGAGTGACGGCCATATGCATGTGCATGGGTAATCTTATCGTAGGAGCCTACTTTAGGATTGTGGCTGATTGTAGCACATGGCATa                                         >  2:332747/1‑141 (MQ=255)
                                                                                        tcACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTTCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATAc                                        <  2:53979/141‑1 (MQ=255)
                                                                                               ataatCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTACGCAt                                 >  2:292755/1‑141 (MQ=255)
                                                                                                taatCAACAGGTACCTTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCAtt                                <  2:165654/141‑1 (MQ=255)
                                                                                                         ggTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGa                       >  2:78904/1‑141 (MQ=255)
                                                                                                         ggTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGa                       >  1:20614/1‑141 (MQ=255)
                                                                                                                 cATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCGTAATAGCCAACTTTAGGACTGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTCATTTGACGCTttga               >  2:198424/1‑141 (MQ=255)
                                                                                                                   tGGTAGCTTCTACCGAATCCATTTCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTttgatt             >  1:202273/1‑141 (MQ=255)
                                                                                                                              aCCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAagta  >  1:238121/1‑141 (MQ=255)
                                                                                                                                          |                                                                                                                                 
GTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATGCTTTCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTA  >  CP000730/1063944‑1064210

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: