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
A6 F1 I0 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 386,449 T→C 20.5% I553I (ATT→ATC)  cstA → carbon starvation protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE386,4490TC20.5% 147.5 / 31.9 73I553I (ATT→ATC) cstAcarbon starvation protein
Reads supporting (aligned to +/- strand):  ref base T (21/37);  new base C (11/4);  total (32/41)
Fisher's exact test for biased strand distribution p-value = 1.77e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.93e-01

TTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGCTCTGTGCCGTGGTGTTGTTCAAGATGAAACGTC  >  minE/386384‑386516
                                                                 |                                                                   
ttCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCaa                                                                >  1:3665008/1‑71 (MQ=255)
 tcctccATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAAc                                                               >  1:568502/1‑71 (MQ=255)
      taTCAGGGCGTGGTTGATCCGCTGGGCGGCGTTAAGAGCCTGTGGCCGCTGTTCGGTATCTCCAACCAGa                                                           <  1:4894737/69‑1 (MQ=255)
      cATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTAtt                                                                     <  1:675295/60‑1 (MQ=255)
       aTCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGAt                                                          >  1:3166269/1‑70 (MQ=255)
       aTCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATg                                                         >  1:5089241/1‑71 (MQ=255)
        tCAGGGCGTGGTTGATCCGCTGGGCGGCGTTAAGAGCCTGTGGCCGCTGTTCGGTATCTCCAACCAGATGc                                                        >  1:512031/1‑71 (MQ=255)
        tCAGGGCGTGGTTGATCCGCTGGGCGGCGTTAAGAGCCTGTGGCCGCTGTTCGGTATCTCCAACCAGATGc                                                        <  1:3424525/71‑1 (MQ=255)
        tCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAAc                                                               <  1:2615699/64‑1 (MQ=255)
        tCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAg                                                            <  1:3803587/67‑1 (MQ=255)
        tCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGc                                                        >  1:3092143/1‑71 (MQ=255)
          aGGTCGTGGTTGATCCGCTGGGCGGCGTTAAGAGCCTGTGGCCGCTGTTCGGTATCTCCAACCAGATGCTg                                                      >  1:4025979/1‑71 (MQ=19)
          aGGGCGTGGTCGATCCGCTGGGCGGGATCAACACCCTGTGGCCGCTGTTCGGCATCGCCAACCAGATGCTg                                                      >  1:598713/1‑71 (MQ=255)
          aGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTAtt                                                                     >  1:2362930/1‑56 (MQ=255)
          aGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTg                                                      >  1:764011/1‑71 (MQ=255)
          aGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTg                                                      >  1:892867/1‑71 (MQ=255)
              cGTGGTTGATCCGCTGGGCGGCGTTAAGAGCCTGTGGCCGCTGTTCGGTATCTCCAACCAGATGCTGGCAg                                                  >  1:5376531/1‑71 (MQ=25)
               gTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAgg                                                 <  1:705262/71‑1 (MQ=255)
               gTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAgg                                                 >  1:5403478/1‑71 (MQ=255)
                   ttgATCCGCTGGGCGGCGTTAAGAGCCTGTGGCCGCTGTTCGGTATCTCCAAc                                                               >  1:943000/3‑53 (MQ=16)
                   ttgATCCGCTGGGCGGCGTTAAGAGCCTGTGGCCGCTGTTCGGTATCTCCAACCAGATGCTgg                                                     <  1:3797837/61‑1 (MQ=19)
                     gATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGgc                                           <  1:2984461/71‑1 (MQ=255)
                         cGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCt                                        <  1:5444251/70‑1 (MQ=255)
                         cGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCt                                        <  1:5492450/70‑1 (MQ=255)
                          gCTGGGCGGCGTTAAGAGCCTGTGGCCGCTGTTCGGTATCTCCAACCAGa                                                           >  1:2204434/1‑50 (MQ=255)
                          gCTGGGCGGCGTTAAGAGCCTGTGGCCGCTGTTCGGTATCTCCAACCAGa                                                           >  1:146458/1‑50 (MQ=255)
                          gCTGGGCGGCGTTAAGAGCCTGTGGCCGCTGTTCGGTATCTCCAACCAGATGCTgg                                                     >  1:1378796/1‑56 (MQ=16)
                          gCTGGGCGGCGTTAAGAGCCTGTGGCCGCTGTTCGGTATCTCCAACCAGATGCTgg                                                     >  1:4957401/1‑56 (MQ=16)
                          gCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGAt                                              <  1:2398335/63‑1 (MQ=255)
                          gCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCt                                        <  1:2758244/69‑1 (MQ=255)
                          gCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCt                                        <  1:146810/69‑1 (MQ=255)
                           cTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGAt                                              <  1:490666/62‑1 (MQ=255)
                              ggcggcATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATg                                    <  1:4941133/69‑1 (MQ=255)
                              ggcggcATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGc                                   <  1:1693235/70‑1 (MQ=255)
                                     ttAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTgg                                                     <  1:3298866/45‑1 (MQ=255)
                                     ttAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGCTCTGTGcc                           <  1:4829369/71‑1 (MQ=255)
                                      aaaCACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATg                                                         >  1:4734756/2‑40 (MQ=255)
                                       aaCACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGCTCTGTGCCgt                         >  1:3141143/1‑71 (MQ=255)
                                       aaCACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGCTCTGTGCCgt                         >  1:1956186/1‑71 (MQ=255)
                                        acacTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGc                                                    >  1:1600008/1‑43 (MQ=255)
                                        acacTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCa                                                   >  1:891339/1‑44 (MQ=255)
                                        acacTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCa                                                   >  1:976486/1‑44 (MQ=255)
                                        acacTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCa                                                   >  1:2459854/1‑44 (MQ=255)
                                        acacTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGCTCtgt                              >  1:5453234/1‑65 (MQ=255)
                                        acacTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGCTCTGTGCCgtg                        >  1:22249/1‑71 (MQ=255)
                                          acTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGCTCTGTGCCgtggc                      <  1:2690552/71‑2 (MQ=255)
                                           ctctGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGCTCTGTGCCgtggtg                     <  1:4502642/71‑1 (MQ=255)
                                            tctGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTg                                                      <  1:4189455/37‑1 (MQ=255)
                                            tctGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTg                                                      <  1:5492434/37‑1 (MQ=255)
                                            tctGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTg                                                      <  1:3029552/37‑1 (MQ=255)
                                            tctGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTg                                                      <  1:2767654/37‑1 (MQ=255)
                                              tgtgGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGCTCTGTGCCGTGgtgt                    <  1:1902847/69‑1 (MQ=255)
                                              tgtgGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGCTCTGTGCCGTGgtgt                    <  1:1909524/69‑1 (MQ=255)
                                                tgGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGCTCTGTGCCGTGGtgttgt                 <  1:2220919/70‑1 (MQ=255)
                                                tgGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGCTCTGTGCCGTGGTgttgtt                <  1:3904189/71‑1 (MQ=255)
                                                  gCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGCTGTGTGCCGTGGTGTTGTTc               >  1:1524396/1‑70 (MQ=255)
                                                  gCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGCTCTGTGCCGTGGTGTTGTTc               <  1:1081807/70‑1 (MQ=255)
                                                   ccGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGCTCTGTGCCGTGGTGTTGTTCaa             <  1:1004850/71‑1 (MQ=255)
                                                   ccGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGCTCTGTGCCGTGGTGTTGTTCaa             <  1:5119035/71‑1 (MQ=255)
                                                    cGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGCTCTGTGCCgtg                        <  1:4678787/59‑1 (MQ=255)
                                                    cGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGCTCTGTGCCgtg                        <  1:1543935/59‑1 (MQ=255)
                                                    cGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGCTCTGTGCCGTGGTGTTGTTCaa             <  1:897326/70‑1 (MQ=255)
                                                      cTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGCTCTGTGCCGTGGTGTTGTTCAAGAt          <  1:4079546/71‑1 (MQ=255)
                                                      cTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGCTCTGTGCCGTGGTGTTGTTCAAGAt          <  1:1507950/71‑1 (MQ=255)
                                                      cTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGCTCTGTGCCGTGGTGTTGTTCAAGAt          <  1:4090526/71‑1 (MQ=255)
                                                         tttGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGCTCTGTGCCGTGGTGTTGTTCAAGATGa        <  1:3445311/70‑1 (MQ=255)
                                                         tttGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGCTCTGTGCCGTGGTGTTGTTCAAGATGa        <  1:4236191/70‑1 (MQ=255)
                                                           cggTATCTCCAACCAGATGCTGGCAGCCGTAGCGCTGATACTGGGCACCGTTGTGCTGATTAAGATGaagc     >  1:42089/2‑69 (MQ=255)
                                                            ggTATCTCCAACCAGATGCTGGCAGCCGTAGCGCTGGTACTGGGCACCGTTGTGCTGATTAAGATGaagc     <  1:3029975/70‑3 (MQ=255)
                                                            ggTATCTCCAACCAGATGCTGGCAGCCGTAGCGCTGGTACTGGGCACCGTTGTGCTGATTAAGATGAAGCg    >  1:4953888/1‑71 (MQ=255)
                                                              tATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGCTCTGTGCCGTGGTGTTGTTCAAGAt          <  1:3022940/63‑1 (MQ=255)
                                                              tATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGCTCTGTGCCGTGGTGTTGTTCAAGAt          <  1:1215862/63‑1 (MQ=255)
                                                              tATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGCTCTGTGCCGTGGTGTTGTTCAAGATGAAACGt   >  1:4084974/1‑70 (MQ=255)
                                                              tATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGCTCTGTGCCGTGGTGTTGTTCAAGATGAAACGt   >  1:1260441/1‑70 (MQ=255)
                                                               aTTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGCTCTGTGCCGTGGTGTTGTTCAAGATGAAACGTc  >  1:169844/1‑70 (MQ=255)
                                                                 |                                                                   
TTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGCTCTGTGCCGTGGTGTTGTTCAAGATGAAACGTC  >  minE/386384‑386516

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