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 1,864,396 A→G 53.5% intergenic (+143/+5) ygcP → / ← ygcQ predicted anti‑terminator regulatory protein/predicted flavoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,864,3960AG53.5% 14.7 / 84.0 101intergenic (+143/+5)ygcP/ygcQpredicted anti‑terminator regulatory protein/predicted flavoprotein
Reads supporting (aligned to +/- strand):  ref base A (28/19);  new base G (17/37);  total (45/56)
Fisher's exact test for biased strand distribution p-value = 5.40e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.88e-01

Only 100 of 105 total aligned reads displayed.

CTTGACGCGTCTTATCAGGCCTACAAGTCCCCAGGCCAGAACCGTAGGCAGGATCATCCGGCAACACGTTATTGGCAATCTGCGTGAATGTTTGTCACCAGTGCCTCCAGCACCACTTTCCAGTCATCAAC  >  minE/1864333‑1864463
                                                               |                                                                   
cTTGACGCGTCTTATCAGGCCTACAAGTCCCCAGGCCAGAACCGTAGGCAGGATCATCCGGCAACACGt                                                                <  1:2072008/69‑1 (MQ=255)
cTTGACGCGTCTTATCAGGCCTACAAGTCCCCAGGCCAGAACCGTAGGCAGGATCATCCGGCAACACGt                                                                <  1:2395648/69‑1 (MQ=255)
cTTGACGCGTCTTATCAGGCCTACAAGTCCCCAGGCCAGAACCGTAGGCAGGATCATCCGGCAACACGt                                                                <  1:2912711/69‑1 (MQ=255)
  tGACGCGTCTTATCAGGCCTACAAGGCCCCAGGCCAGAACCGTAGGCAGGATCATCCGGCAACACGt                                                                <  1:1526401/67‑1 (MQ=255)
         tCTTATCAGGCCTACAAGTCCCCAGGCCAGAACCGTAGGCAGGATCATCCGGCAACACGt                                                                <  1:201574/60‑1 (MQ=255)
         tCTTATCAGGCCTACAAGTCCCCAGGCCAGAACCGTAGGCAGGATCATCCGGCAACACGTTATTGGCaa                                                       >  1:1119705/1‑69 (MQ=255)
         tCTTATCAGGCCTACAAGTCCCCAGGCCAGAACCGTAGGCAGGATCATCCGGCAACACGTTATTGGCaa                                                       >  1:163106/1‑69 (MQ=255)
         tCTTATCAGGCCTACAAGTCCCCAGGCCAGAACCGTAGGCAGGATCATCCGGCAACACGTTATTCGCaa                                                       >  1:34184/1‑69 (MQ=255)
                  gcttACAAGTCCCCAGCCCAGAACCGTAGGCAGGATCATCCGGCAGCACGTTATTGGCAATCTGCGTg                                               <  1:3305050/65‑1 (MQ=39)
                  gcttACAAGTCCCCAGCCCAGAACCGTAGGCAGGATCATCCGGCAGCACGTTATTGGCAATCTGCGTg                                               <  1:3198353/65‑1 (MQ=39)
                  gcttACAAGTCCCCAGCCCAGAACCGTAGGCAGGATCATCCGGCAGCACGTTATTGGCAATCTGCGTg                                               <  1:3418769/65‑1 (MQ=39)
                  gcttACAAGTCCCCAGCCCAGAACCGTAGGCAGGATCATCCGGCAGCACGTTATTGGCAATCTGCGTg                                               <  1:408249/65‑1 (MQ=39)
                  gcttACAAGTCCCCAGCCCAGAACCGTAGGCAGGATCATCCGGCAGCACGTTATTGGCAATCTGCGTg                                               <  1:2295269/65‑1 (MQ=39)
                  gcttACAAGTCCCCAGCCCAGAACCGTAGGCAGGATCATCCGGCAGCACGTTATTGGCAATCTGCGTg                                               <  1:2224978/65‑1 (MQ=39)
                  gcttACAAGTCCCCAGCCCAGAACCGTAGGCAGGATCATCCGGCAGCACGTTATTGGCAATCTGCGTg                                               <  1:737936/65‑1 (MQ=39)
                  gcttACAAGTCCCCAGCCCAGAACCGTAGGCAGGATCATCCGGCAGCACGTTATTGGCAATCTGCGTg                                               <  1:1891487/65‑1 (MQ=39)
                  gcttACAAGTCCCCAGCCCAGAACCGTAGGCAGGATCATCCGGCAGCACGTTATTGGCAATCTGCGTg                                               <  1:168049/65‑1 (MQ=39)
                  gcttACAAGTCCCCAGCCCAGAACCGTAGGCAGGATCATCCGGCAGCACGTTATTGGCAATCTGCGTg                                               <  1:1663745/65‑1 (MQ=39)
                  gcttACAAGTCCCCAGCCCAGAACCGTAGGCAGGATCATCCGGCAGCACGTTATTGGCAATCTGCGTg                                               <  1:868925/65‑1 (MQ=39)
                  gcttACAAGTCCCCAGCCCAGAACCGTAGGCAGGATCATCCGGCAGCACGTTATTGGCAATCTGCGTg                                               <  1:1235142/65‑1 (MQ=39)
                  gcttACAAGTCCCCAGCCCAGAACCGTAGGCAGGATCATCCGGCAGCACGTTATTGGCAATCTGCGTg                                               <  1:1292005/65‑1 (MQ=39)
                  gCCTACAAGTCCCCAGGCCAGAACCGTAGGCAGGATCATCCGGCAACACGTTATTgg                                                          >  1:2246534/1‑57 (MQ=255)
                  gCCTACAAGTCCCCAGGCCAGAACCGTAGGCAGGATCATCCGGCAACACGTTATTGGCAATCTGCGTGa                                              >  1:2907971/1‑69 (MQ=255)
                  gCCTACAAGTCCCCAGGACAGAACCGTAGGCAGGATCATCCGTCAACACGTTATTGGCAATCTGCGTg                                               >  1:2798431/1‑68 (MQ=39)
                     tACAAGTCCCCCGCCCAGAACCGTAGGCAGGATCATCCGGCAGCACGt                                                                >  1:1240182/1‑48 (MQ=37)
                     tACAAGTCCCCAGCCCAGAACCGTAGGCAGGATCATCCGGCAgcac                                                                  >  1:2931851/1‑46 (MQ=37)
                     tACAAGTCCCCAGCCCAGAACCGTAGGCAGGATCATCCGGCAGCACg                                                                 >  1:1863301/1‑47 (MQ=37)
                     tACAAGTCCCCAGCCCAGAACCGTAGGCAGGATCATCCGGCAGCACg                                                                 >  1:2372804/1‑47 (MQ=37)
                     tACAAGTCCCCAGCCCAGAACCGTAGGCAGGATCATCCGGCAGCACGt                                                                >  1:2404741/1‑48 (MQ=37)
                     tACAAGTCCCCAGCCCAGAACCGTAGGCAGGATCATCCGGCAGCACGt                                                                >  1:1896610/1‑48 (MQ=37)
                     tACAAGTCCCCAGCCCAGAACCGTAGGCAGGATCATCCGGCAGCACGt                                                                >  1:2043992/1‑48 (MQ=37)
                     tACAAGTCCCCAGCCCAGAACCGTAGGCAGGATCATCCGGCAGCACGt                                                                >  1:136285/1‑48 (MQ=37)
                     tACAAGTCCCCAGCCCAGAACCGTAGGCAGGATCATCCGGCAGCACGt                                                                >  1:368684/1‑48 (MQ=37)
                     tACAAGTCCCCAGCCCAGAACCGTAGGCAGGATCATCCGGCAGCACGt                                                                >  1:3248181/1‑48 (MQ=37)
                     tACAAGTCCCCAGCCCAGAACCGTAGGCAGGATCATCCGGCAGCACGt                                                                >  1:1059245/1‑48 (MQ=37)
                     tACAAGTCCCCAGCCCAGAACCGTAGGCAGGATCATCCGGCAGCACGt                                                                >  1:1066549/1‑48 (MQ=37)
                     tACAAGTCCCCAGCCCAGAACCGTAGGCAGGATCATCCGGCAGCACGt                                                                >  1:1880086/1‑48 (MQ=37)
                     tACAAGTCCCCAGCCCAGAACCGTAGGCAGGATCATCCGGCAGCACGt                                                                >  1:1444037/1‑48 (MQ=37)
                     tACAAGTCCCCAGCCCAGAACCGTAGGCAGGATCATCCGGCAGCACGt                                                                >  1:779225/1‑48 (MQ=37)
                     tACAAGTCCCCAGCCCAGAACCGTAGGCAGGATCATCCGGCAGCACGt                                                                >  1:1020653/1‑48 (MQ=37)
                     tACAAGTCCCCAGCCCAGAACCGTAGGCAGGATCATCCGGCAGCACGt                                                                >  1:1552910/1‑48 (MQ=37)
                       cAAGTCCCCAGGCCAGAACCGTAGGCAGGATCATCCGGCAACACGTTATTGGCAATCTGCGTGAATGtt                                         >  1:2040633/1‑69 (MQ=255)
                       cAAGTCCCCAGGCCAGAACCGTAGGCAGGATCATCCGGCAACACGTTATTGGCAATCTGCGTGAATGtt                                         >  1:2106305/1‑69 (MQ=255)
                       cAAGTCCCCAGGCCAGAACCGTAGGCAGGATCATCCGGCAACACGTTATTGGCAATCTGCGTGAATGtt                                         >  1:120448/1‑69 (MQ=255)
                       cAAGTCCCCAGGCCAGAACCGTAGGCAGGATCATCCGGCAACACGTTATTGGCAATCTGCGTGAATGtt                                         >  1:1213930/1‑69 (MQ=255)
                             cccAGGCCAGAACCGTAGGCAGGATCATCCGGCAACACGTTATTGGCAATCTGCGTGAATGTTTGTc                                     >  1:2583770/1‑67 (MQ=255)
                             cccAGGCCAGAACCGTAGGCAGGATCATCCGGCAACACGTTATTGGCAATCTGCGTGAATGTTTGTc                                     >  1:2680231/1‑67 (MQ=255)
                             cccAGGCCAGAACCGTAGGCAGGATCATCCGGCAACACGTTATTGGCAATCTGCGTGAATGTTTGTc                                     >  1:1268342/1‑67 (MQ=255)
                             cccAGGCCAGAACCGTAGGCAGGATCATCCGGCAACACGTTATTGGCAATCTGCGTGAATGTTTGTc                                     >  1:2872290/1‑67 (MQ=255)
                             cccAGGCCAGAACCGTAGGCAGGATCATCCGGCAACACGTTATTGGCAATCTGCGTGAATGTTTGTc                                     >  1:797418/1‑67 (MQ=255)
                             cccAGGCCAGAACCGTAGGCAGGATCATCCGGCAACACGTTATTGGCAATCTGCGTGAATGTTTGTc                                     >  1:3087446/1‑67 (MQ=255)
                             cccAGGCCAGAACCGTAGGCAGGATCATCCGGCAACACGTTATTGGCAATCTGCGTGAATGTTTGTc                                     >  1:1543623/1‑67 (MQ=255)
                             cccAGGCCAGAACCGTAGGCAGGATCATCCGGCAACACGTTATTGGCAATCTGCGTGAATGTTTGTc                                     >  1:1154854/1‑67 (MQ=255)
                             cccAGGCCAGAACCGTAGGCAGGATCATCCGGCAACACGTTATTGGCAATCTGCGTGAATGTTTGTc                                     >  1:819908/1‑67 (MQ=255)
                             cccAGGCCAGAACCGTAGGCAGGATCATCCGGCAACACGTTATTGGCAATCTGCGTGAATGTTTGTc                                     >  1:3248637/1‑67 (MQ=255)
                             cccAGGCCAGAACCGTAGGCAGGATCATCCGGCAACACGTTATTGGCAATCTGCGTGAATGTTTGTc                                     >  1:1752308/1‑67 (MQ=255)
                             cccAGGCCAGAACCGTAGGCAGGATCATCCGGCAACACGTTATTGGCAATCTGCGTGAATGTTTGTc                                     >  1:1869118/1‑67 (MQ=255)
                             cccAGGCCAGAACCGTAGGCAGGATCATCCGGCAACACGTTATTGGCAATCTGCGTGAATGTTTGTc                                     >  1:1222702/1‑67 (MQ=255)
                             cccAGGCCAGAACCGTAGGCAGGATCATCCGGCAACACGTTATTGGCAATCTGCGTGAATGTTTGTc                                     >  1:1208304/1‑67 (MQ=255)
                             cccAGGCCAGAACCGTAGGCAGGATCATCCGGCAACACGTTATTGGCAATCTGCGTGAATGTTTGTCAc                                   <  1:2444988/69‑1 (MQ=255)
                             cccAGGCCAGAACCGTAGGCAGGATCATCCGGCAACACGTTATTGGCAATCTGCGTGAATGTTTGTCAc                                   <  1:420090/69‑1 (MQ=255)
                             cccAGGCCAGAACCGTAGGCAGGATCATCCGGCAACACGTTATTGGCAATCTGCGTGAATGTTTGTCAc                                   <  1:1320493/69‑1 (MQ=255)
                             cccAGGCCAGAACCGTAGGCAGGATCATCCGGCAACACGTTATTGGCAATCTGCGTGAATGTTTGTCAc                                   <  1:3002172/69‑1 (MQ=255)
                             cccAGGCCAGAACCGTAGGCAGGATCATCCGGCAACACGTTATTGGCAATCTGCGTGAATGTTTGTCAc                                   <  1:2453431/69‑1 (MQ=255)
                             cccAGGCCAGAACCGTAGGCAGGATCATCCGGCAACACGTTATTGGCAATCTGCGTGAATGTTTGTCAc                                   <  1:3138813/69‑1 (MQ=255)
                             cccAGGCCAGAACCGTAGGCAGGATCATCCGGCAACACGTTATTGGCAATCTGCGTGAATGTTTGTCAc                                   <  1:670544/69‑1 (MQ=255)
                             cccAGGCCAGAACCGTAGGCAGGATCATCCGGCAACACGTTATTGGCAATCTGCGTGAATGTTTGTCAc                                   <  1:355455/69‑1 (MQ=255)
                             cccAGGCCAGAACCGTAGGCAGGATCATCCGGCAACACGTTATTGGCAATCTGCGTGAATGTTTGTCAc                                   <  1:2040145/69‑1 (MQ=255)
                             cccAGGCCAGAACCGTAGGCAGGATCATCAGGCAACAAGTTATTGGCAATCTGCGTGAATGTTTGTCAc                                   <  1:1996002/69‑1 (MQ=255)
                                              ggCAGGATCATCCGGCAGCACGTTATTGGCAATCTGCGTg                                               <  1:108476/40‑1 (MQ=255)
                                                    atcatcCGGCAACACGTTATTGGCAATCTGCGTGAATGTTTGTCAc                                   <  1:411184/46‑1 (MQ=255)
                                                     tcatcCGGCAGCACGTTATTGGCAATCTGCGTGAATGGTTGTCACCa                                 <  1:40271/47‑1 (MQ=38)
                                                     tcatcCGGCAGCACGTTATTGGCAATCTGCGTGAATGGTTGTCACCa                                 <  1:348437/47‑1 (MQ=38)
                                                     tcatcCGGCAGCACGTTATTGGCAATCTGCGTGAATGGTTGTCACCa                                 <  1:1015649/47‑1 (MQ=38)
                                                     tcatcCGGCAGCACGTTATTGGCAATCTGCGTGAATGGTTGTCACCa                                 <  1:642610/47‑1 (MQ=38)
                                                     tcatcCGGCAGCACGTTATTGGCAATCTGCGTGAATGGTTGTCACCa                                 <  1:481892/47‑1 (MQ=38)
                                                     tcatcCGGCAGCACGTTATTGGCAATCTGCGTGAATGGTTGTCACCa                                 <  1:636345/47‑1 (MQ=38)
                                                     tcatcCGGCAGCACGTTATTGGCAATCTGCGTGAATGGTTGTCACCa                                 <  1:577430/47‑1 (MQ=38)
                                                     tcatcCGGCAGCACGTTATTGGCAATCTGCGTGAATGGTTGTCACCa                                 <  1:2453896/47‑1 (MQ=38)
                                                     tcatcCGGCAGCACGTTATTGGCAATCTGCGTGAATGGTTGTCACCa                                 <  1:141190/47‑1 (MQ=38)
                                                     tcatcCGGCAGCACGTTATTGGCAATCTGCGTGAATGGTTGTCACCa                                 <  1:1336512/47‑1 (MQ=38)
                                                     tcatcCGGCAGCACGTTATTGGCAATCTGCGTGAATGGTTGTCACCa                                 <  1:1549966/47‑1 (MQ=38)
                                                     tcatcCGGCAGCACGTTATTGGCAATCTGCGTGAATGGTTGTCACCa                                 <  1:1586277/47‑1 (MQ=38)
                                                     tcatcCGGCAGCACGTTATTGGCAATCTGCGTGAATGGTTGTCACCa                                 <  1:1768963/47‑1 (MQ=38)
                                                     tcatcCGGCAGCACGTTATTGGCAATCTGCGTGAATGGTTGTCACCa                                 <  1:1797959/47‑1 (MQ=38)
                                                     tcatcCGGCAGCACGTTATTGGCAATCTGCGTGAATGGTTGTCACCa                                 <  1:2290904/47‑1 (MQ=38)
                                                     tcatcCGGCAGCACGTTATTGGCAATCTGCGTGAATGGTTGTCACCa                                 <  1:3393730/47‑1 (MQ=38)
                                                     tcatcCGGCAGCACGTTATTGGCAATCTGCGTGAATGGTTGTCACCa                                 <  1:246156/47‑1 (MQ=38)
                                                     tcatcCGGCAGCACGTTATTGGCAATCTGCGTGAATGGTTGTCACCa                                 <  1:2864809/47‑1 (MQ=38)
                                                     tcatcCGGCAGCACGTTATTGGCAATCTGCGTGAATGGTTGTCACCa                                 <  1:301706/47‑1 (MQ=38)
                                                     tcatcCGGCAGCACGTTATTGGCAATCTGCGTGAATGGTTGTCACCa                                 <  1:3154777/47‑1 (MQ=38)
                                                     tcatcCGGCAGCACGTTATTGGCAATCTGCGTGAATGGTTGTCACCa                                 <  1:3250986/47‑1 (MQ=38)
                                                     tcatcCGGCAGCACGTTATTGGCAATCTGCGTGAATGGTTGTCACCa                                 <  1:3324237/47‑1 (MQ=38)
                                                      catcCGGCAACACGTTATTGGCAATCTGCGTGAATGTTTGt                                      >  1:733558/1‑41 (MQ=255)
                                                      catcCGGCAACACGTTATTGGCAATCTGCGTGAATGTTTGTCACCAGTGCCTCCAGCACCACTTTCCa           >  1:3211494/1‑68 (MQ=255)
                                                            gCAACACGTTATTGGCAATCTGCGTGAATGTTTGTCACCAGTGCCTCCAGCACCACTTTCCAGtcatc     <  1:565027/68‑1 (MQ=255)
                                                            gCAACACGTTATTGGCAATCTGCGTGAATGTTTGTCACCAGTGCCTCCAGCACCACTTTCCAGtcatc     <  1:1057203/68‑1 (MQ=255)
                                                            gCAACACGTTATTGGCAATCTGCGTGAATGTTTGTCACCAGTGCCTCCAGCACCACTTTCCAGtcatc     <  1:1322834/68‑1 (MQ=255)
                                                              aaCACGTTATTGGCAATCTGCGTGAATGTTTGTCACCAGTGCCTCCAGCACCACTTTCCAGTCATCAAc  <  1:2695859/69‑1 (MQ=255)
                                                              aaCACGTTATTGGCAATCTGCGTGAATGTTTGTCACCAGTGCCTCCAGCACCACTTTCCAGTCATCAAc  <  1:792311/69‑1 (MQ=255)
                                                               |                                                                   
CTTGACGCGTCTTATCAGGCCTACAAGTCCCCAGGCCAGAACCGTAGGCAGGATCATCCGGCAACACGTTATTGGCAATCTGCGTGAATGTTTGTCACCAGTGCCTCCAGCACCACTTTCCAGTCATCAAC  >  minE/1864333‑1864463

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A