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 2,835,320 C→T 20.7% D193N (GAC→AAC)  yjeJ ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,835,3200CT20.7% 126.0 / 21.3 86D193N (GAC→AAC) yjeJhypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (39/29);  new base T (8/10);  total (47/39)
Fisher's exact test for biased strand distribution p-value = 4.26e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.38e-01

CGCTAAATTGTTCTTTGCCACTTTCATCTTTAAAGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTGTCCTGGCA  >  minE/2835260‑2835386
                                                            |                                                                  
cgcTAAATTGTTCTTTGCCACTTTCATCTTTAAAGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGt                                                            >  1:3264651/1‑69 (MQ=255)
cgcTAAATTGTTCTTTGCCACTTTCATCTTTAAAGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGt                                                            >  1:2654021/1‑69 (MQ=255)
cgcTAAATTGTTCTTTGCCACTTTCATCTTTAAAGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGt                                                            >  1:2230794/1‑69 (MQ=255)
  cTAAATTGTTCTTTGCCACTTTCATCTTTAAAGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTa                                                          <  1:117498/69‑1 (MQ=255)
  cTAAATTGTTCTTTGCCACTTTCATCTTTAAAGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTa                                                          <  1:2721361/69‑1 (MQ=255)
  cTAAATTGTTCTTTGCCACTTTCATCTTTAAAGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTa                                                          <  1:1353583/69‑1 (MQ=255)
  cTAAATTGTTCTTTGCCACTTTCATCTTTAAAGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTa                                                          <  1:2886682/69‑1 (MQ=255)
  cTAAATTGTTCTTTGCCACTTTCATCTTTAAAGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTa                                                          <  1:7067/69‑1 (MQ=255)
  cTAAATTGTTCTTTGCCACTTTCATCTTTAAAGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTa                                                          <  1:702565/69‑1 (MQ=255)
  cTAAATTGTTCTTTGCCACTTTCATCTTTAAAGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTa                                                          <  1:1725771/69‑1 (MQ=255)
       ttGTTCTTTGCCACTTTCATCTTTAAAGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTATGttt                                                     <  1:1323244/69‑1 (MQ=255)
       ttGTTCTTTGCCACTTTCATCTTTAAAGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTATGttt                                                     <  1:327078/69‑1 (MQ=255)
        tGTTCTTTGCCACTTTCATCTTTAAAGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTATGTTTc                                                    <  1:2504803/69‑1 (MQ=255)
                   aCTTTCATCTTTAAAGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTATGTTTCCATTCCGGTTg                                         <  1:1985558/69‑1 (MQ=255)
                     tttCATCTTTAAAGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTATGTTTCCATTCCGGTTggg                                       <  1:3055559/69‑1 (MQ=255)
                      ttCATCTTTAAAGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTATGTTTCCATTCCGGTTggg                                       >  1:2558304/1‑68 (MQ=255)
                      ttCATCTTTAAAGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTATGTTTCCATTCCGGTTggg                                       >  1:1626535/1‑68 (MQ=255)
                      ttCATCTTTAAAGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTATGTTTCCATTCCGGTTggg                                       >  1:3017512/1‑68 (MQ=255)
                            tttAAAGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTATGTTTc                                                    <  1:2900942/49‑1 (MQ=255)
                            tttAAAGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTATGTTTc                                                    <  1:2937040/49‑1 (MQ=255)
                            tttAAAGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTATGTTTc                                                    <  1:3216540/49‑1 (MQ=255)
                             ttAAAGCGGTAAAGCACCGCCAGATAATGGTCGATCAAGTTATGTTTc                                                    <  1:1309737/48‑1 (MQ=255)
                                aaGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGgtg                               <  1:2579174/66‑1 (MQ=255)
                                aaGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGgtg                               <  1:548673/66‑1 (MQ=255)
                                aaGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGgtg                               <  1:1328900/66‑1 (MQ=255)
                                      tAAAGCACCGCCAGATAATGGTTGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCatat                         >  1:3187304/1‑66 (MQ=255)
                                      tAAAGCACCGCCAGATAATGGTTGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCatat                         >  1:1603062/1‑66 (MQ=255)
                                      tAAAGCACCGCCAGATAATGGTTGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCatat                         >  1:3390501/1‑66 (MQ=255)
                                      tAAAGCACCGCCAGATAATGGTTGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCatat                         >  1:2258261/1‑66 (MQ=255)
                                      tAAAGCACCGCCAGATAATGGTTGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCatat                         >  1:1568250/1‑66 (MQ=255)
                                      tAAAGCACCGCCAGATAATGGTTGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCatat                         >  1:2834726/1‑66 (MQ=255)
                                      tAAAGCACCGCCAGATAATGGTTGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCatat                         >  1:25030/1‑66 (MQ=255)
                                      tAAAGCACCGCCAGATAATGGTTGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCata                          >  1:2841553/1‑65 (MQ=255)
                                       aaaGCACCGCCAGATAATGGTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCatat                         >  1:834438/1‑65 (MQ=255)
                                       aaaGCACCGCCAGATAATGGTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCatat                         >  1:2875067/1‑65 (MQ=255)
                                       aaaGCACCGCCAGATAATGGTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCa                     <  1:585755/69‑1 (MQ=255)
                                                    aTAATGGTTGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTTTc        <  1:695182/69‑1 (MQ=255)
                                                    aTAATGGTTGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTTTc        <  1:980007/69‑1 (MQ=255)
                                                    aTAATGGTTGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTTTc        <  1:943987/69‑1 (MQ=255)
                                                    aTAATGGTTGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTTTc        <  1:811650/69‑1 (MQ=255)
                                                    aTAATGGTTGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTTTc        <  1:3185181/69‑1 (MQ=255)
                                                    aTAATGGTTGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTTTc        <  1:326800/69‑1 (MQ=255)
                                                    aTAATGGTTGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTTTc        <  1:2602370/69‑1 (MQ=255)
                                                    aTAATGGTTGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTTTc        <  1:2403442/69‑1 (MQ=255)
                                                    aTAATGGTTGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTTTc        <  1:239975/69‑1 (MQ=255)
                                                    aTAATGGTTGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTTTc        <  1:2102636/69‑1 (MQ=255)
                                                      aaTGTTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCa                            <  1:1901904/47‑1 (MQ=255)
                                                      aaTGGTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCa                            <  1:2798098/47‑1 (MQ=255)
                                                      aaTGGTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCa                            <  1:1433137/47‑1 (MQ=255)
                                                      aaTGGTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCa                            <  1:286103/47‑1 (MQ=255)
                                                      aaTGGTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCa                            <  1:3229770/47‑1 (MQ=255)
                                                      aaTGGTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCa                            <  1:2219005/47‑1 (MQ=255)
                                                      aaTGGTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCa                            <  1:655963/47‑1 (MQ=255)
                                                      aaTGGTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCa                            <  1:1501860/47‑1 (MQ=255)
                                                         ggTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCa                            <  1:1954100/44‑1 (MQ=255)
                                                         ggTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTGTCCTgg    >  1:2414724/1‑68 (MQ=255)
                                                         ggTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTGTCCTGGc   >  1:2282596/1‑69 (MQ=255)
                                                         ggTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTGTCCTGGc   >  1:514136/1‑69 (MQ=255)
                                                         ggTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTGTCCTGGc   >  1:2176215/1‑69 (MQ=255)
                                                         ggTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTGTCCTGGc   >  1:1479428/1‑69 (MQ=255)
                                                         ggTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTGTCCTGGc   >  1:926802/1‑69 (MQ=255)
                                                         ggTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTGTCCTGGc   >  1:1203576/1‑69 (MQ=255)
                                                          gTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTcc                      >  1:50264/1‑49 (MQ=255)
                                                          gTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCa                     >  1:1970818/1‑50 (MQ=255)
                                                          gTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCa                     >  1:632117/1‑50 (MQ=255)
                                                          gTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCa                     >  1:820931/1‑50 (MQ=255)
                                                          gTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCa                     >  1:1222049/1‑50 (MQ=255)
                                                          gTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCa                     >  1:2582766/1‑50 (MQ=255)
                                                          gTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCa                     >  1:2774299/1‑50 (MQ=255)
                                                          gTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCa                     >  1:2880820/1‑50 (MQ=255)
                                                          gTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCa                     >  1:3111894/1‑50 (MQ=255)
                                                          gTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCa                     >  1:2393122/1‑50 (MQ=255)
                                                          gTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTGTCCTGGCa  >  1:1580593/1‑69 (MQ=255)
                                                          gTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTGTCCTGGCa  >  1:2461169/1‑69 (MQ=255)
                                                          gTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTGTCCTGGCa  >  1:885669/1‑69 (MQ=255)
                                                          gTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTGTCCTGGCa  >  1:2832063/1‑69 (MQ=255)
                                                          gTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTGTCCTGGCa  >  1:14785/1‑69 (MQ=255)
                                                          gTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTGTCCTGGCa  >  1:217313/1‑69 (MQ=255)
                                                          gTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTGTCCTGGCa  >  1:3327888/1‑69 (MQ=255)
                                                          gTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTGTCCTGGCa  >  1:2022104/1‑69 (MQ=255)
                                                          gTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTGTCCTGGCa  >  1:63110/1‑69 (MQ=255)
                                                          gTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTGTCCTGGCa  >  1:1704479/1‑69 (MQ=255)
                                                          gTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTGTCCTGGCa  >  1:554845/1‑69 (MQ=255)
                                                          gTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTGTCCTGGCa  >  1:1783532/1‑69 (MQ=255)
                                                          gTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTGTCCTGGCa  >  1:2018241/1‑69 (MQ=255)
                                                          gTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTGTCCTGGCa  >  1:1972166/1‑69 (MQ=255)
                                                            |                                                                  
CGCTAAATTGTTCTTTGCCACTTTCATCTTTAAAGCGGTAAAGCACCGCCAGATAATGGTCGAACAAGTTATGTTTCCATTCCGGTTGGGAATAGGTGTCATATTCCAGATTGCCATTGTCCTGGCA  >  minE/2835260‑2835386

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