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
A20 F999 I0 R1 98 154.1 11406411 97.3% 11098437 49.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,063,143 T→C A299A (GCT→GCC)  yihN → putative transporter YihN

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,063,1430TC77.3% 344.3 / 107.8 163A299A (GCT→GCC) yihNputative transporter YihN
Reads supporting (aligned to +/- strand):  ref base T (22/15);  new base C (65/61);  total (87/76)
Fisher's exact test for biased strand distribution p-value = 4.56e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.44e-01

Only 100 of 173 total aligned reads displayed.

TGAAATCGCCAAGTAAATATCTATGCTACACCTTTATCATTAGTACCGCTGCGCTCGTACTGTTGATTATGCTGCCGCACGAAAGTATGCCGGTCT  >  NC_000913/4063094‑4063189
                                                 |                                              
tGAAATCGCCAAGTAAATATCTATGCTACACCTTTATCATTAGTACCGCt                                                >  1:3675659/1‑50 (MQ=255)
  aaaTCGCCAAGTAAATATCTATGCTACACCTTTATCATTAGTACcgccgc                                              >  1:3588719/1‑50 (MQ=255)
  aaaTCGCCAAGTAAATATCTATGCTACACCTTTATCATTAGTACcgccgc                                              >  2:3711402/1‑50 (MQ=255)
  aaaTCGCCAAGTAAATATCTATGCTACACCTTTATCATTAGTACcgccgc                                              <  1:4669200/50‑1 (MQ=255)
  aaaTCGCCAAGTAAATATCTATGCTACACCTTTATCATTAGTACcgccgc                                              >  2:212046/1‑50 (MQ=255)
   aaTCGCCAAGTAAATATCTATGCTACACCTTTATCATTAGTACCGCcgcg                                             <  2:3587104/50‑1 (MQ=255)
    aTCGCCAAGTAAATATCTATGCTACACCTTTATCATTAGTACCGCCgcgc                                            >  1:1684827/1‑50 (MQ=255)
    aTCGCCAAGTAAATATCTATGCTACACCTTTATCATTAGTACCGCCgcgc                                            >  2:373155/1‑50 (MQ=255)
        ccAAGTAAATATCTATGCTACACCTTTATCATTAGTACCGCTGCGCTCGt                                        <  2:122221/50‑1 (MQ=255)
        ccAAGTAAATATCTATGCTACACCTTTATCATTAGTACCGCCGCGCTCg                                         >  1:4704132/1‑49 (MQ=255)
        ccAAGTAAATATCTATGCTACACCTTTATCATTAGTACCGCCGCGCTCGt                                        <  1:4254675/50‑1 (MQ=255)
         cAAGTAAATATCTATGCTACACCTTTATCATTAGTTCCGCCGCGCTCGTa                                       <  2:667879/50‑1 (MQ=255)
         cAAGTAAATATCTATGCTACACCTTTATCATTAGTACCGCCGCGCTCGTa                                       >  2:1536731/1‑50 (MQ=255)
         cAAGTAAATATCTATGCTACACCTTTATCATTAGTACCGCCGCGCTCGTa                                       >  2:106835/1‑50 (MQ=255)
         cAAGTAAATATCTATGCTACACCTTTATCATTAGTACCGCCGCGCTCGTa                                       >  1:4852972/1‑50 (MQ=255)
         cAAGTAAATATCTATGCTACACCTTTATCATTAGTACCGCCGCGCTCGTa                                       >  2:3111033/1‑50 (MQ=255)
           aGTAAATATCTATGCTACACCTTTATCATTAGTACCGCTGCGCTCGTACt                                     <  2:3697174/50‑1 (MQ=255)
           aGTAAATATCTATGCTACACCTTTATCATTAGTACCGCCGCGCTCGTACt                                     >  2:2841631/1‑50 (MQ=255)
            gTAAATATCTATGCTACACCTTTATCATTAGTACCGCCGCGCTCGTACTg                                    >  2:3762617/1‑50 (MQ=255)
             tAAATATCTATGCTACACCTTTATCATTAGTACCGCTGCGCTCGTACTGt                                   >  2:1555228/1‑50 (MQ=255)
             tAAATATCTATGCTACACCTTTATCATTAGTACCGCCGCGCTCGTACTGt                                   >  2:1683226/1‑50 (MQ=255)
             tAAATATCTATGCTACACCTTTATCATTAGTACCGCCGCGCTCGTACTGt                                   <  1:1195407/50‑1 (MQ=255)
              gaaTATCTATGCTACACCTTTATCATTAGTACCGCCGCGCACGTACTGtt                                  >  2:2211909/2‑50 (MQ=255)
               aaTATCTATGCTACACCTTTATCATTAGTACCGCCGCGCTCGTACTTTTg                                 <  2:2325471/50‑1 (MQ=255)
               aaTATCTATGCTACACCTTTATCATTAGTACCGCCGCGCTCGTACTGTTg                                 <  1:3473278/50‑1 (MQ=255)
                 tatCTATGCTACACCTTTATCATTAGTACCGCTGCGCTCGTACTGTTGAt                               >  2:2654936/1‑50 (MQ=255)
                 tatCTATGCTACACCTTTATCATTAGTACCGCCGCGCTCGTACTGTTGAt                               <  1:1733465/50‑1 (MQ=255)
                  atCTATGCTACACCTTTATCATTAGTACCGCCGCGCTCGTACTGTTGAt                               >  1:2663992/1‑49 (MQ=255)
                   tCTATGCTACACCTTTATCATTAGTCCCGCCGCGCTCGTACTGTTGAtt                              <  1:2456609/49‑1 (MQ=255)
                   tCTATGCTACACCTTTATCATTAGTACCGCCGCGCTCGTACTGTTGAtt                              <  2:5175037/49‑1 (MQ=255)
                   tCTATGCTACACCTTTATCATTAGTACCGCCGCGCTCGTACTGTTGAtt                              <  2:3428865/49‑1 (MQ=255)
                   tCTATGCTACACCTTTATCATTAGTACCGCCGCGCTCGTACTGTTGATTa                             >  1:227369/1‑50 (MQ=255)
                   tCTATGCTACACCTTTATCATTAGTACCGCCGCGCTCGTACTGTTGATTa                             >  1:1410404/1‑50 (MQ=255)
                   tCTATGCTACACCTTTATCATTAGTACCGCCGCGCTCGTACTGTTGATTa                             >  2:2909704/1‑50 (MQ=255)
                   tCTATGCTACACCTTTATCATTAGTACCGCCGCGCTCGTACTGTTGATTa                             >  1:83445/1‑50 (MQ=255)
                      aTGCTACACCTTTATCATTAGTACCGCCGCGCTCGTACTGTTGATTAtgc                          >  1:4717803/1‑50 (MQ=255)
                      aTGCTACACCTTTATCATTAGTACCGCCGCGCTCGTACTGTTGATTAtgc                          >  2:1195817/1‑50 (MQ=255)
                      aTGCTACACCCTTATCATTAGTACCGCCGCGCTCGTACTGTTGATTAtgc                          >  2:5112640/1‑50 (MQ=255)
                       tGCTACACCTTTATCATTAGTACCGCTGCGCTCGTACTGTTGATTAtgct                         >  2:603065/1‑50 (MQ=255)
                       tGCTACACCTTTATCATTAGTACCGCTGCGCTCGTACTGTTGATTAt                            <  2:2363086/47‑1 (MQ=255)
                       tGCTACACCTTTATCATTAGTACCGCTGCGCTCGTACTGTTGATTAt                            <  1:890769/47‑1 (MQ=255)
                       tGCTACACCTTTATCATTAGTACCGCTGCGCTCGTACTGTTGATTAt                            <  2:2249732/47‑1 (MQ=255)
                       tGCTACACCTTTATCATTAGTACCGCCGCGCTCGTACTGTTGATTAtgct                         >  1:5419856/1‑50 (MQ=255)
                       tGCTACACCTTTATCATTAGTACCGCCGCGCTCGTACTGTTGATTAt                            <  2:2624052/47‑1 (MQ=255)
                         cTACACCTTTATCATTAGTACCGCTGCGCTCGTACTGTTGATTAtgctgc                       >  1:2703525/1‑50 (MQ=255)
                         cTACACCTTTATCATTAGTACCGCCGCGCTCGTACTGTTGATTAtgctg                        <  1:2014880/49‑1 (MQ=255)
                          tACACCTTTATCATTAGTACCGCTGCGCTCGTACTGTTGATTATGCTGcc                      >  2:1707896/1‑50 (MQ=255)
                          tACACCTTTATCATTAGTACCGCCGCGCTCGTACTGTTGATTATGCTGcc                      >  1:2988606/1‑50 (MQ=255)
                            cgccTTTATCAATAGTGCCGCCGCGCTCGTACTGTTGATTATGCTGCCGc                    <  2:660231/48‑1 (MQ=37)
                            cacCTTTATCATTAGTACCGCCGCGCTCGTACTGTTGATTATGCTGcc                      <  2:3188992/48‑1 (MQ=255)
                            cacCTTTATCATTAGTACCGCCGCGCTCGTACTGTTGATTATGCTGCCg                     >  1:756951/1‑49 (MQ=255)
                            cacCTTTATCATTAGTACCGCCGCGCTCGTACTGTTGATTATGCTGCCGc                    <  2:565277/50‑1 (MQ=255)
                            cacCTTTATCATTAGTACCGCCGCGCTCGTACTGTTGATTATGCTGCCGc                    <  2:3488954/50‑1 (MQ=255)
                             acCTTTATCATTAGTACCGCCGCGCTCGTACTGTTGATTATGCTGCCGCa                   >  1:4553291/1‑50 (MQ=255)
                              ccTTTATCATTAGTACCGCTGCGCTCGTACTGTTGATTATGCTGCCGCAc                  <  1:5104534/50‑1 (MQ=255)
                              ccTTTATCATTAGTACCGCCGCGCTCGTACTGTTGATTATGCTGCCGCAc                  >  2:878401/1‑50 (MQ=255)
                              ccTTTATCATTAGTACCGCCGCGCTCGTACTGTTGATTATGCTGCCGCAc                  >  1:5586190/1‑50 (MQ=255)
                               cTTTATCATTAGTACCGCCGCGCTCGTACTGTTGATTATGCTGCCGCAc                  >  2:4235208/1‑49 (MQ=255)
                               cTTTATCATTAGTACCGCCGCGCTCGTACTGTTGATTATGCTGCCGCAc                  >  1:2556875/1‑49 (MQ=255)
                               cTTTATCATTAGTACCGCCGCGCTCGTACTGTTGATTATGCTGCCGCACg                 <  1:1931716/50‑1 (MQ=255)
                               cTTTATCATTAGTACCGCCGCGCTCGTACTGTTGATTATGCTGCCGCACg                 <  2:2919644/50‑1 (MQ=255)
                                tttATCATTAGTACCGCCGCGCTCGTACTGTTGATTATGCTGCCGCACg                 >  1:544151/1‑49 (MQ=255)
                                tttATCATTAGTACCGCCGCGCTCGTACTGTTGATTATGCTGCCGCACg                 >  2:2478299/1‑49 (MQ=255)
                                tttATCATTAGTACCGCCGCGCTCGTACTGCTGATTATGCTCCCGCACg                 >  2:2086427/1‑49 (MQ=38)
                                 ttATCATTAGTACCGCTGCGCTCGTACTGTTGATTATGCTGCCGCACGa                >  2:4032093/1‑49 (MQ=255)
                                 ttATCATTAGTACCGCCGCGCTCGTACTGTTGATTATGCTGCCGCACGa                >  1:177644/1‑49 (MQ=255)
                                  tATCATTAGTACCGCTGCGCTCGTACTGTTGATTATGCTGCCGCACGaa               <  1:1719186/49‑1 (MQ=255)
                                  tATCATTAGTACCGCTGCGCTCGTACTGTTGATTATGCTGCCGCACGa                >  2:1747521/1‑48 (MQ=255)
                                  tATCATTAGTACCGCTGCGCTCGTACTGTTGATTATGCTGCCGCACGa                <  1:4542793/48‑1 (MQ=255)
                                  tATCATTAGTACCGCCGCGCTCGTACTGTTGATTATGCTGCCGCACGaa               <  1:505486/49‑1 (MQ=255)
                                  tATCATTAGTACCGCCGCGCTCGTACTGTTGATTATGCTGCCGCACGa                >  1:2005638/1‑48 (MQ=255)
                                  tATCATTAGTACCGCCGCGCTCGTACTGTTGATTATGCTGCCGCACGa                <  2:314277/48‑1 (MQ=255)
                                   aTCATTATTACAGCCGCGCTCGTACTGTTGATTTTGCCGCCGCACGAAAg             >  2:4911603/1‑50 (MQ=25)
                                   aTCATTAGTACCGCCGCGCTCGTACTGTTGATTATGCTGCCGCACGaaa              <  1:3385831/49‑1 (MQ=255)
                                   aTCATTAGTACCGCCGCGCTCGTACTGTTGATTATGCTGCCGCACGAAAg             >  2:3215211/1‑50 (MQ=255)
                                    tCATTAGTACCGCTGCGCTCGTACTGTTGATTATGCTGCCGCACGAAAGt            <  2:2048995/50‑1 (MQ=255)
                                    tCATTAGTACCGCCGCGCTCGTACTGTTGATTATGCTGCCGCACGAAAGt            <  1:3244888/50‑1 (MQ=255)
                                     cATTAGTACCGCTGCGCTCGTACTGTTGATTATGCTGCCGCACGAAAGTa           >  2:1640763/1‑50 (MQ=255)
                                     cATTAGTACCGCCGCGCTCGTACTGTTGATTATGCTGCCGCACGAAAGTa           >  2:1617439/1‑50 (MQ=255)
                                      aTTAGTACCGCTGCGCTCGTACTGTTGATTATGCTGCCGCACGAAAGTAt          >  2:2567909/1‑50 (MQ=255)
                                      aTTAGTACCGCTGCGCTCGTACTGTTGATTATGCTGCCGCACGAAAGTAt          >  2:1982097/1‑50 (MQ=255)
                                      aTTAGTACCGCCGCGCTCGTACTGTTGATTATGCTGCCGCACGAAAGTAt          <  2:3280206/50‑1 (MQ=255)
                                      aTTAGTACCGCCGCGCTCGTACTGTTGATTATGCTGCCGCACGAAAGTAt          <  1:1042752/50‑1 (MQ=255)
                                       ttAGTACCGCTGCGCTCGTACTGTTGATTATGCTGCCGCACGAAAGTATg         <  1:3705485/50‑1 (MQ=255)
                                       ttAGTACCGCTGCGCTCGTACTGTTGATTATGCTGCCGCACGAAAGTATg         >  1:2952519/1‑50 (MQ=255)
                                       ttAGTACCGCCGCGCTCGTACTGTTGATTATGCTGCCGCACGAAAGTATg         >  1:324040/1‑50 (MQ=255)
                                       ttAGTACCGCCGCGCTCGTACTGTTGATTATGCTGCCGCACGAAAGTATg         >  1:4087827/1‑50 (MQ=255)
                                       ttAGTACCGCCGCGCTCGTACTGTTGATTATGCTGCCGCACGAAAGTATg         <  1:3270321/50‑1 (MQ=255)
                                       ttAGTACCGCCGCGCTCGTACTGTTGATTATGCTGCCGCACGAAAGTATg         <  2:4292305/50‑1 (MQ=255)
                                       ttAGTACCGCCGCGCTCGTACTGTTGATTATGCTGCCGCACGAAAGTATg         >  1:2698632/1‑50 (MQ=255)
                                         aGTACCGCCGCGCTCGTACTGTTGATTATGCTGCCGCACGAAAGTATGc        <  1:4888379/49‑1 (MQ=255)
                                         aGTACCGCCGCGCTCGTACTGTTGATTATGCTGCCGCACGAAAGTATGc        <  2:397299/49‑1 (MQ=255)
                                          gTACCGCCGCGCTCGTGCTGTTGATTATGCTGCCGCACGAAAGTATGcc       <  2:707973/49‑1 (MQ=38)
                                          gTACCGCCGCGCTCGTACTGTTGATTATGCTGCCGCACGAAAGTATGcc       <  2:4859741/49‑1 (MQ=255)
                                          gTACCGCCGCGCTCGTACTGTTGATTATGCTGCCGCACGAAAGTATGcc       <  1:507148/49‑1 (MQ=255)
                                          gTACCGCCGCGCTCGTACTGTTGATTATGCTGCCGCACGAAAGTATGCCg      <  2:1185379/50‑1 (MQ=255)
                                            aCCGCCGCGCTCGTACTGTTGATTATGCTGCCGCACGAAAGTATGCCGGt    >  2:4137011/1‑50 (MQ=255)
                                            aCCGCCGCGCTCGTACTGTTGATTATGCTGCCGCACGAAAGTATGCCGGt    >  1:4726475/1‑50 (MQ=255)
                                            aCCGCCGCGCTCGTACTGTTGATTATGCTGCCGCACGAAAGTATGCCGGt    >  1:5551798/1‑50 (MQ=255)
                                              cgccgcGCTCGTACTGTTGATTATGCTGCCGCACGAAAGTATGCCGGTCt  <  1:2390528/50‑1 (MQ=255)
                                                 |                                              
TGAAATCGCCAAGTAAATATCTATGCTACACCTTTATCATTAGTACCGCTGCGCTCGTACTGTTGATTATGCTGCCGCACGAAAGTATGCCGGTCT  >  NC_000913/4063094‑4063189

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A