Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 402,421 C→T 27.9% P114P (CCG→CCA)  rlpA ← minor lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE402,4210CT27.9% 88.8 / 32.5 82P114P (CCG→CCA) rlpAminor lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (29/30);  new base T (12/11);  total (41/41)
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

CGATCATTAATGCGCACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCGAATGCTTCGCCAGAGGCCGTCAGGTTACT  >  minE/402353‑402489
                                                                    |                                                                    
cgATCATTAATGCGCACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATc                                                                      <  1:466533/69‑1 (MQ=255)
cgATCATTAATGCGCACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATc                                                                      <  1:1918073/69‑1 (MQ=255)
cgATCATTAATGCGCACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATc                                                                      <  1:621741/69‑1 (MQ=255)
    cATTAATGCGCACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGaa                                                                  >  1:2713119/1‑69 (MQ=255)
    cATTAATGCGCACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGaa                                                                  >  1:2763588/1‑69 (MQ=255)
    cATTAATGCGCACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGaa                                                                  >  1:692085/1‑69 (MQ=255)
    cATTAATGCGCACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGaa                                                                  >  1:2040923/1‑69 (MQ=255)
    cATTAATGCGCACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGaa                                                                  >  1:869105/1‑69 (MQ=255)
    cATTAATGCGCACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGaa                                                                  >  1:1957597/1‑69 (MQ=255)
    cATTAATGCGCACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGaa                                                                  >  1:358678/1‑69 (MQ=255)
        aaTGCGCACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGGTCGGAAGCGt                                                              >  1:3107767/1‑69 (MQ=255)
        aaTGCGCACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGt                                                              >  1:2630088/1‑69 (MQ=255)
        aaTGCGCACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGt                                                              >  1:2227880/1‑69 (MQ=255)
        aaTGCGCACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGt                                                              >  1:2210440/1‑69 (MQ=255)
        aaTGCGCACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGt                                                              >  1:406827/1‑69 (MQ=255)
           gcgcACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCTTTg                                                            <  1:1239432/68‑1 (MQ=255)
           gcgcACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTg                                                            <  1:460869/68‑1 (MQ=255)
           gcgcACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTg                                                            <  1:973157/68‑1 (MQ=255)
           gcgcACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTg                                                            <  1:425039/68‑1 (MQ=255)
           gcgcACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTg                                                            <  1:2476219/68‑1 (MQ=255)
           gcgcACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTg                                                            <  1:1806396/68‑1 (MQ=255)
           gcgcACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTg                                                            <  1:199320/68‑1 (MQ=255)
                  acGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCgg                                                                    >  1:219049/1‑53 (MQ=255)
                  acGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCgg                                                                    >  1:422418/1‑53 (MQ=255)
                  acGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCt                                                    >  1:1182645/1‑69 (MQ=255)
                  acGATCATTCGCCAGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCgg                                                                    >  1:1098043/1‑53 (MQ=255)
                       cATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGt                                               <  1:290044/69‑1 (MQ=255)
                       cATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGt                                               <  1:1268807/69‑1 (MQ=255)
                       cATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGt                                               <  1:1104614/69‑1 (MQ=255)
                       cATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGt                                               <  1:637922/69‑1 (MQ=255)
                       cATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGt                                               <  1:42939/69‑1 (MQ=255)
                       cATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGt                                               <  1:3036366/69‑1 (MQ=255)
                       cATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGt                                               <  1:3036513/69‑1 (MQ=255)
                       cATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGt                                               <  1:3107094/69‑1 (MQ=255)
                       cATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGt                                               <  1:2040457/69‑1 (MQ=255)
                       cATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGt                                               <  1:2033016/69‑1 (MQ=255)
                       cATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGt                                               <  1:3124410/69‑1 (MQ=255)
                       cATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGt                                               <  1:1697393/69‑1 (MQ=255)
                        aTTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGt                                               <  1:1753807/68‑1 (MQ=255)
                          tCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCa                                             >  1:1597855/1‑68 (MQ=255)
                          tCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAg                                            >  1:1000212/1‑69 (MQ=255)
                          tCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAg                                            >  1:488834/1‑69 (MQ=255)
                          tCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAg                                            >  1:1552158/1‑69 (MQ=255)
                          tCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAg                                            >  1:1488208/1‑69 (MQ=255)
                            gCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGTGATTGGAAGCGTTGGATGGGCCGCCGt                                               >  1:2071737/1‑64 (MQ=39)
                            gCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATTGGAAGCg                                                               >  1:2822654/1‑48 (MQ=255)
                            gCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATTGGAAGCGt                                                              >  1:1436965/1‑49 (MQ=255)
                            gCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGt                                               >  1:3395396/1‑64 (MQ=255)
                            gCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTc                                              >  1:2551327/1‑65 (MQ=255)
                            gCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTc                                              >  1:3378078/1‑65 (MQ=255)
                            gCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTc                                              >  1:578810/1‑65 (MQ=255)
                            gCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTc                                              >  1:3245024/1‑65 (MQ=255)
                            gCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTc                                              >  1:1359775/1‑65 (MQ=255)
                            gCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTc                                              >  1:430022/1‑65 (MQ=255)
                            gCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTc                                              >  1:2402175/1‑65 (MQ=255)
                            gCCCGTTAGCCAGCTTAGTGATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTc                                              >  1:2146022/1‑65 (MQ=255)
                                       aGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCg                               <  1:924781/69‑1 (MQ=255)
                                       aGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCg                               <  1:2147862/69‑1 (MQ=255)
                                       aGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCg                               <  1:2703464/69‑1 (MQ=255)
                                       aGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCg                               <  1:2316265/69‑1 (MQ=255)
                                       aGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCg                               <  1:730776/69‑1 (MQ=255)
                                        ggTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCg                               <  1:1337781/68‑1 (MQ=255)
                                        ggTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCg                               <  1:482531/68‑1 (MQ=255)
                                        ggTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCg                               <  1:948595/68‑1 (MQ=255)
                                        ggTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCg                               <  1:1619540/68‑1 (MQ=255)
                                        ggTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCg                               <  1:2212511/68‑1 (MQ=255)
                                               gATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTCAACTGTGTCGGATCGAAAGCTTc                       <  1:614126/69‑1 (MQ=255)
                                               gATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTCAACTGTGTCGGATCGAAAGCTTc                       <  1:935301/69‑1 (MQ=255)
                                               gATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTCAACTGTGTCGGATCGAAAGCTTc                       <  1:818027/69‑1 (MQ=255)
                                               gATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTCAACTGTGTCGGATCGAAAGCTTc                       <  1:1017732/69‑1 (MQ=255)
                                               gATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTCAACTGTGTCGGATCGAAAGCTTc                       <  1:658763/69‑1 (MQ=255)
                                               gATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTCAACTGTGTCGGATCGAAAGCTTc                       <  1:3343576/69‑1 (MQ=255)
                                               gATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTCAACTGTGTCGGATCGAAAGCTTc                       <  1:3322893/69‑1 (MQ=255)
                                               gATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTCAACTGTGTCGGATCGAAAGCTTc                       <  1:3182526/69‑1 (MQ=255)
                                               gATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTCAACTGTGTCGGATCGAAAGCTTc                       <  1:3033369/69‑1 (MQ=255)
                                               gATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTCAACTGTGTCGGATCGAAAGCTTc                       <  1:2040722/69‑1 (MQ=255)
                                               gATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTCAACTGTGTCGGATCGAAAGCTTc                       <  1:1671126/69‑1 (MQ=255)
                                                         tAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCtgt                                        >  1:1716445/1‑42 (MQ=255)
                                                         tAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCGAATGCTTCGCCagag                >  1:2422958/1‑66 (MQ=255)
                                                         tAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCGAATGCTTCGCCAGAGGcc             >  1:3146556/1‑69 (MQ=255)
                                                         tAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCGAATGCTTCGCCAGAGGcc             >  1:2946713/1‑69 (MQ=255)
                                                         tAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCGAATGCTTCGCCAGAGGcc             >  1:216056/1‑69 (MQ=255)
                                                         tAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCGAATGCTTCGCCAGAGGcc             >  1:1559347/1‑69 (MQ=255)
                                                         tAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCGAATGCTTCGCCAGAGGcc             >  1:1062652/1‑69 (MQ=255)
                                                         tAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCGAATGCTTCGCCAGAGGcc             >  1:974659/1‑69 (MQ=255)
                                                                    cGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCGAATGCTTCGCCAGAGGCCGTCAGGTTACt  >  1:53299/1‑69 (MQ=255)
                                                                    cGGAAGCGGTGGATGGGCTGCCGTCAGCTGTGTCGGGTCGAATGCTTCGCCAGAGGCCGTCAGGTTACt  >  1:2809471/1‑69 (MQ=255)
                                                                    |                                                                    
CGATCATTAATGCGCACCACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCGAATGCTTCGCCAGAGGCCGTCAGGTTACT  >  minE/402353‑402489

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: ‑

GATK/CNVnator alignment

N/A