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
A5 F3 I0 R2 52 68.8 5189613 98.4% 5106579 62.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,824,326 T→C 100% pseudogene (459/687 nt) rph → ECK3633:JW3618:b3643; ribonuclease PH

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,824,3260TC100.0% 288.8 / NA 81pseudogene (459/687 nt)rphECK3633:JW3618:b3643; ribonuclease PH
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (41/40);  total (41/40)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CGGGTGCCTGCGTGGCGCTGGTAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTG  >  W3110S.gb/3824259‑3824392
                                                                   |                                                                  
cGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAAccc                                                                  <  1:4660798/70‑1 (MQ=255)
cGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAAccc                                                                  <  1:3093114/70‑1 (MQ=255)
cGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAAccc                                                                  <  1:4450720/70‑1 (MQ=255)
  ggTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGAt                                                               <  1:4700747/71‑1 (MQ=255)
  ggTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGAt                                                               <  1:4706494/71‑1 (MQ=255)
  ggTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGAt                                                               <  1:4995134/71‑1 (MQ=255)
   gTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGa                                                                <  1:1188667/69‑1 (MQ=255)
    tGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa                                                             <  1:2839921/71‑1 (MQ=255)
     gCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa                                                             >  1:4331568/1‑70 (MQ=255)
      ccTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGaaa                                                           <  1:148901/71‑1 (MQ=255)
      ccTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGaa                                                            <  1:4858775/70‑1 (MQ=255)
      ccTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa                                                             <  1:2431608/69‑1 (MQ=255)
       cTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAg                                                          >  1:2152120/1‑71 (MQ=255)
        tGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATg                                                              <  1:3475845/66‑1 (MQ=255)
        tGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAgg                                                         >  1:256943/1‑71 (MQ=255)
        tGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAg                                                          >  1:833112/1‑70 (MQ=255)
         gCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa                                                             <  1:1342032/66‑1 (MQ=255)
          cGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGaaa                                                           >  1:4128498/1‑67 (MQ=255)
          cGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGa                                                       >  1:2908556/1‑71 (MQ=255)
          cGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGa                                                       <  1:1950969/71‑1 (MQ=255)
          cGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGa                                                       <  1:3308488/71‑1 (MQ=255)
            tGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATg                                                     <  1:4586568/71‑1 (MQ=255)
            tGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATg                                                     <  1:841418/71‑1 (MQ=255)
             ggCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGAt                                                               >  1:1054700/1‑60 (MQ=255)
              gcgcTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGt                                                   <  1:2365600/71‑1 (MQ=255)
                gcTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa                                                             >  1:4835398/1‑59 (MQ=255)
                 cTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGc                                                <  1:3034536/71‑1 (MQ=255)
                   ggcaGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGc                                                >  1:1227549/4‑69 (MQ=255)
                   ggcaGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCg                                              >  1:1334818/4‑71 (MQ=255)
                     caGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCa                                            <  1:2427116/70‑1 (MQ=255)
                        aTGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAAccc                                                                  <  1:440052/46‑1 (MQ=255)
                        aTGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa                                                             <  1:3517422/51‑1 (MQ=255)
                        aTGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa                                                             <  1:1315595/51‑1 (MQ=255)
                          gcgcTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTc                                       >  1:1892642/1‑71 (MQ=255)
                           cgcTACAGAAGCGGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCt                                      <  1:4724701/71‑1 (MQ=255)
                           cccTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCt                                      <  1:4856672/69‑1 (MQ=255)
                            gcTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTg                                     <  1:2438318/71‑1 (MQ=255)
                             cTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGt                                    <  1:179369/71‑1 (MQ=255)
                              tACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTc                                   >  1:1494426/1‑71 (MQ=255)
                              tACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTc                                   >  1:1967009/1‑71 (MQ=255)
                              tACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTc                                   >  1:3516955/1‑71 (MQ=255)
                               aCAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCg                                  >  1:4067378/1‑71 (MQ=255)
                                cAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTc                                   <  1:3513259/69‑1 (MQ=255)
                                cAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCgg                                 >  1:1348096/1‑71 (MQ=255)
                                cAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCg                                  <  1:4942679/70‑1 (MQ=255)
                                  gAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAg                                                          <  1:4271216/44‑1 (MQ=255)
                                        ggtggAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATtgta                          >  1:2422156/1‑69 (MQ=255)
                                        ggtggAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATtg                            >  1:3001891/1‑68 (MQ=255)
                                        ggtggAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATtg                            >  1:3130421/1‑68 (MQ=255)
                                         gtggAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGa                                                       <  1:1290000/40‑1 (MQ=255)
                                          tggAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGAt                                                      <  1:3313086/40‑1 (MQ=255)
                                           ggAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGc                                             <  1:3188032/48‑1 (MQ=255)
                                            gAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTc                                   >  1:931705/1‑57 (MQ=255)
                                            gAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACgg                     <  1:1559541/71‑1 (MQ=255)
                                            gAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACg                      >  1:1585793/1‑70 (MQ=255)
                                             aaaaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggt                    >  1:3517808/1‑70 (MQ=255)
                                              aaaCGGCAAGCTGAAAACCAACCCGATGAAAGGGa                                                       >  1:388714/1‑35 (MQ=255)
                                              aaaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATgg                                                    >  1:4942342/1‑38 (MQ=255)
                                              aaaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATgg                                                    >  1:1641921/1‑38 (MQ=255)
                                              aaaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggtg                   <  1:575993/71‑3 (MQ=255)
                                              aaaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggt                    >  1:1680206/1‑69 (MQ=255)
                                              aaaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggt                    >  1:2695312/1‑69 (MQ=255)
                                               aaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggtg                   >  1:1010980/1‑68 (MQ=255)
                                               aaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggtg                   >  1:1300576/1‑68 (MQ=255)
                                               aaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGa                  <  1:3366249/71‑1 (MQ=255)
                                                aCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggtg                   >  1:3370152/1‑67 (MQ=255)
                                                 cGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAg                >  1:3188039/1‑71 (MQ=255)
                                                   gCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGca              <  1:1802321/71‑2 (MQ=255)
                                                   gCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGca              <  1:4108775/71‑2 (MQ=255)
                                                   gCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGc               >  1:3018105/1‑70 (MQ=255)
                                                    cAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGcaa             <  1:4857688/71‑3 (MQ=255)
                                                     aaGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCggta                               >  1:1970664/1‑50 (MQ=255)
                                                     aaGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGcaat            <  1:1003899/71‑4 (MQ=255)
                                                     aaGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGcaat            >  1:4172466/1‑68 (MQ=255)
                                                        cTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTg         <  1:1277418/71‑1 (MQ=255)
                                                         tGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGt                                    <  1:1036026/43‑1 (MQ=255)
                                                          gAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAAc                       >  1:572915/1‑55 (MQ=255)
                                                          gAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGa                  >  1:2425853/1‑60 (MQ=255)
                                                          gAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGc        >  1:3925391/1‑70 (MQ=255)
                                                          gAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGc        >  1:1083984/1‑70 (MQ=255)
                                                          gAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGc        >  1:2099437/1‑70 (MQ=255)
                                                           aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg       <  1:593508/70‑1 (MQ=255)
                                                           aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGa      >  1:2164117/1‑71 (MQ=255)
                                                            aaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGa      <  1:1523096/70‑1 (MQ=255)
                                                             aaccaaccCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATc    <  1:3854110/71‑1 (MQ=255)
                                                             aaccaaccCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATc    >  1:4865450/1‑71 (MQ=255)
                                                               ccAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTg  >  1:2753080/1‑71 (MQ=255)
                                                                   |                                                                  
CGGGTGCCTGCGTGGCGCTGGTAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTG  >  W3110S.gb/3824259‑3824392

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