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 F17 I0 R2 278 43.2 2215644 94.6% 2095999 61.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,364,103 A→G 30.6% W456R (TGG→CGG)  trkH ← potassium transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,364,1030AG30.6% 96.0 / 62.0 72W456R (TGG→CGG) trkHpotassium transporter
Reads supporting (aligned to +/- strand):  ref base A (38/12);  new base G (16/6);  total (54/18)
Fisher's exact test for biased strand distribution p-value = 7.74e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCGGGGTAAAGAGCACCAGCAATGTAAAGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCATTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGCAACCACGCCAAGCCCTGGCCCCAGGTTATTCAA  >  minE/2364034‑2364172
                                                                     |                                                                     
tCGGGGTAAAGAGCACCAGCAATGTAAAGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCAt                                                                      >  1:168398/1‑71 (MQ=255)
     gTAAAGAGCACCAGCAATGTAAAGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCAt                                                                      >  1:1904397/1‑66 (MQ=255)
        aaGAGCACCAGCAATGTAAAGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCATTTAGCCAc                                                              >  1:1206171/1‑71 (MQ=255)
          gagCACCAGCAATGTAAAGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCATTTAGCCAcag                                                            >  1:734614/1‑69 (MQ=255)
          gagCACCAGCAATGTAAAGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCATTTAGCCACCg                                                            >  1:697443/1‑71 (MQ=255)
           agCACCAGCAATGTAAAGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGttt                                                                    >  1:199421/1‑62 (MQ=255)
              aCCAGCAATGTAAAGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCATTTAGCCACCGGGtt                                                        <  1:7610/71‑1 (MQ=255)
              aCCAGCAATGTAAAGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCATTTAGCCACCGGGtt                                                        <  1:431190/71‑1 (MQ=255)
                 aGCAATGTAAAGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCATTTAGCCACCGGGTTCa                                                      >  1:32400/1‑70 (MQ=255)
                  gCAATGTAAAGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATa                                                    >  1:437653/1‑71 (MQ=255)
                        tAAAGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCa                                                      <  1:1844005/63‑1 (MQ=255)
                        tAAAGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCATTTAGCCAc                                                              >  1:2144879/1‑55 (MQ=255)
                        tAAAGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCATTTAGCCACCGGGTTCATACTGGt                                               >  1:128868/1‑70 (MQ=255)
                        tAAAGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCATTTAGCCACCGGGTTCATACTGGt                                               >  1:1984893/1‑70 (MQ=255)
                        tAAAGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCATTTAGCCACCGGGTTCATACTGGt                                               >  1:655905/1‑70 (MQ=255)
                         aaaGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATAc                                                   >  1:1597588/1‑65 (MQ=255)
                         aaaGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATAc                                                   >  1:2082774/1‑65 (MQ=255)
                         aaaGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATAc                                                   >  1:69099/1‑65 (MQ=255)
                          aaGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCATTTAGCCACCg                                                            >  1:2045819/1‑55 (MQ=255)
                          aaGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCATTTAGCCACCGGGTTCATACTGGTaa                                             <  1:1746046/70‑1 (MQ=255)
                              ccTCGAGACGACCAAACAGGATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGTTa                                        >  1:1418591/1‑71 (MQ=255)
                              ccTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCATTTAGCCACCGGGTTCATACTGGTAAAGtt                                         <  1:664585/70‑1 (MQ=255)
                               cTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCATTTAGCCACCGGGTTCATACTGGTAAAGTTAt                                       <  1:2177975/71‑1 (MQ=255)
                                tCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCATTTAGCCACCGGGTTCa                                                      <  1:872664/55‑1 (MQ=255)
                                tCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCATTTAGCCACCGGGTTCATACTGGTAAAGTTAt                                       >  1:542139/1‑70 (MQ=255)
                                 cGAGACGACCAAACAGCATTTTGGCAATCAGGATCCATTTAGCCACCGGGTTCATACTGGTAAAGTTAt                                       >  1:213754/1‑69 (MQ=255)
                                 cGAGACGACCAAACAGCATGTTGGCTATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGTTAt                                       >  1:1873776/1‑69 (MQ=255)
                                 cGAGACGACCAAACAGCATGTTGGCAATCAGGATCCa                                                                       >  1:1510549/1‑37 (MQ=255)
                                 cGAGACGACCAAACAGCATGTTGGCAATCAGGATCCa                                                                       >  1:1329063/1‑37 (MQ=255)
                                  gagaCGACCAAACAGCATGTTGGCAATCAGGATCCa                                                                       >  1:1826301/1‑36 (MQ=255)
                                  gagaCGACCAAACAGCATGTTGGCAATCAGGATCCATTTAGcc                                                                >  1:704592/1‑43 (MQ=255)
                                  gagaCGACCAAACAGCATGTTGGCAATCAGGATCCATTTAGCCa                                                               >  1:876864/1‑44 (MQ=255)
                                  gagaCGACCAAACAGCATGTTGGCAATCAGGATCCATTTAGCCa                                                               >  1:445148/1‑44 (MQ=255)
                                  gagaCGACCAAACAGCATGTTGGCAATCAGGATCCATTTAGCCa                                                               >  1:587074/1‑44 (MQ=255)
                                  gagaCGACCAAACAGCATGTTGGCAATCAGGATCCATTTAGCCACCGGGTTCATACTGGTAAAGTTATCAg                                    >  1:1787535/1‑71 (MQ=255)
                                  gagaCGACCAAACAGCATGTTGGCAATCAGGATCCATTTAGCCACCGGGTTCATACTGGTAAAGTTATCAg                                    >  1:1513211/1‑71 (MQ=255)
                                  gagaCGACCAAACAGCATGTTGGCAATCAGGATCCATTTAGCCACCGGGTTCATACTGGTAAAGTTATCAg                                    >  1:1390623/1‑71 (MQ=255)
                                  gagaCGACCAAACAGCATGTTGGCAATCAGGATCCATTTAGCCACCGGGTTCATACTGGTAAAGTTATCAg                                    >  1:1187583/1‑71 (MQ=255)
                                  gagaCGACCAAACAGCATGTTGGCAAT‑AGGATCCATTTAGCCa                                                               >  1:563203/1‑43 (MQ=39)
                                    gacgacCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGc                                   >  1:770810/1‑70 (MQ=255)
                                    gacgacCAAACAGCATGTTGGCAATCAGGATCCATTTAGCCACCGGGTTCATa                                                    >  1:699152/1‑53 (MQ=255)
                                    gacgacAAAACAGCATGTTGGCAATCAGGATCCATTTAGCCACCGGGTTCATa                                                    >  1:2041533/1‑53 (MQ=255)
                                       gacCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGCAAc                                >  1:2082501/1‑70 (MQ=255)
                                       gacCAAACAGCATGTTGGCAATCAGGATCCATTTAGCCAcc                                                             >  1:965772/1‑41 (MQ=255)
                                       gacCAAACAGCATGTTGGCAATCAGGATCCATTTAGCCACCGGGTTCATACTGGTAAAGTTAt                                       >  1:1285847/1‑63 (MQ=255)
                                       gacCAAACAGCATGTTGGCAATCAGGATCCATTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGCAAc                                >  1:160243/1‑70 (MQ=255)
                                        acCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGCAACCa                              >  1:1031799/1‑71 (MQ=255)
                                        acCAAACAGCATGTTGGCAATCAGGATCCATTTAGCCACCGGGTTCAt                                                     >  1:668436/1‑48 (MQ=255)
                                            aaCAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGtt                                                        <  1:2029522/41‑1 (MQ=255)
                                             aCAGCATGTTGGCAATCATGATCCATTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGCAACCACGcc                          >  1:1515178/1‑70 (MQ=255)
                                             aCAGCATGTTGGCAATCAGGATCCATTTAGCCACCGGGTTCATACTGGTAAAGt                                          >  1:769870/1‑54 (MQ=255)
                                             aCAGCATGTTGGCAATCAGGATCCATTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGCAACCACGcc                          >  1:1383975/1‑70 (MQ=255)
                                              cAGCATGTTGGCAATCAGGATCCATTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGCAACCACGCCaa                        <  1:792130/71‑1 (MQ=255)
                                              cAGCATGTTGGCAATCAGGATCCATTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGCAACCACGCCaa                        <  1:1464080/71‑1 (MQ=255)
                                               aGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCa                                                      >  1:1555111/1‑40 (MQ=255)
                                               aGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCa                                                      >  1:1382246/1‑40 (MQ=255)
                                               aGCATGTTGGCAATCAGGATCCATTTAGCCACCGGGTTCATa                                                    >  1:119751/1‑42 (MQ=255)
                                               aGCATGTTGGCAATCAGGATCCATTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGCAACCa                              >  1:1946804/1‑64 (MQ=255)
                                               aGCATGTTGGCAATCAGGATCCATTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGCAACCa                              >  1:654342/1‑64 (MQ=255)
                                                gCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTgg                                                <  1:869620/45‑1 (MQ=255)
                                                 cATGTTGGCAATCAGGATCCATTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGCAACCACGCCAAGcc                     <  1:1191652/71‑1 (MQ=255)
                                                   tGTTGGCAATCAGGATCCATTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGCAACCACGCCAAGCCCt                   <  1:1227617/71‑1 (MQ=255)
                                                    gTTGGCAATCAGGATCCATTTAGCCACCGGGTTCa                                                      >  1:718146/1‑35 (MQ=255)
                                                     ttGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGCAACCACGCCAAGCCCTgg                 >  1:284300/1‑71 (MQ=255)
                                                     ttGGCAATCAGGATCCATTTAGCCACCGGGTTCATAc                                                   <  1:1954051/37‑1 (MQ=255)
                                                        gCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGCAACCACGCCAAGCCCTGGccc              >  1:1600469/1‑71 (MQ=255)
                                                           aTCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGCAACCACGCCAAg                       <  1:615831/59‑1 (MQ=255)
                                                             cAGGATCCATTTAGCCACCGGGTTCATACTGGTAAAGTTAt                                       >  1:1894694/1‑41 (MQ=255)
                                                              aGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGCAACCACGCCAAGCCCTGGCCCCAGGt         <  1:153649/70‑1 (MQ=255)
                                                              aGGATCCATTTAGCCTCCGGGTTCATACTGGTAAAGTTATCAGCAACCACGCCAAGCCCTGGCCCCAGGt         <  1:1791919/70‑1 (MQ=255)
                                                                gATCCGTTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGCAACCACGCCAAGCCCTGGCCCCAGGTTAt      <  1:1155677/71‑1 (MQ=255)
                                                                gATCCATTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGCAACCACGCCAAGCCCTGGCCCCAGGTTa       >  1:707664/1‑70 (MQ=255)
                                                                 aTCCGTTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGCAACCACGCCAAGCCCTGGcccc             >  1:1823528/1‑63 (MQ=255)
                                                                  tCCGTTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGCAACCACGCCAAGCCCTGGCCCCAGGTTAtt     >  1:1553981/1‑70 (MQ=255)
                                                                   ccATTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGCAACCACGCCAAGCCCTGGCCCCAGGTTATTc    >  1:1518505/1‑70 (MQ=255)
                                                                     aTTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGCAACCACGCCAAGCCCTGGCCCCAGGTTATTCaa  >  1:1450879/1‑70 (MQ=255)
                                                                     |                                                                     
TCGGGGTAAAGAGCACCAGCAATGTAAAGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCATTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGCAACCACGCCAAGCCCTGGCCCCAGGTTATTCAA  >  minE/2364034‑2364172

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