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
A10 F44 I1 R1 19 65.8 3201541 96.2% 3079882 99.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,189,448 C→T Q1367* (CAG→TAG)  rpoC → RNA polymerase, beta prime subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,189,4480CT98.5% 234.5 / NA 67Q1367* (CAG→TAG) rpoCRNA polymerase, beta prime subunit
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base T (30/36);  minor base G (0/1);  total (30/37)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGCAGCCGTTGCGGGCAAACGCGACGAACTGCGCGGCCTGAAAGAGAACGTTATCGTGGGTCGTCTGATCCCGGCAGGTACCGGTTACGCGTACCACCAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGCTGCACCGCAGGTGACTGCAGAAGACGCATCTGCCAGCCTGGCAGAACTGCTGAAC  >  NC_000913/4189351‑4189543
                                                                                                 |                                                                                               
agcagcCGTTGCGGGCAAACGCGACGAACTGCGCGGCCTGAAAGAGAACGTTATCGTGGGTCGTCTGATCCCGGCAGGTACCGGTTACGCGTACCACTAg                                                                                               <  1:1434026/100‑1 (MQ=255)
 gcagcCGTTGCGGGCAAACGCGACGAACTGCGCGGCCTGAAAGAGAACGTTATCGTGGGTCGTCTGATCCCGGCAGGTACCGGTTACGCGTACCACTAgg                                                                                              <  2:1541823/100‑1 (MQ=255)
 gcagcCGTTGCGGGCAAACGCGACGAACTGCGCGGCCTGAAAGAGAACGTTATCGTGGGTCGTCTGATCCCGGCAGGTACCGGTTACGCGTACCACTAgg                                                                                              >  1:618025/1‑100 (MQ=255)
  cagcCGTTGCGGGCAAACGCGACGAACTGCGCGGCCTGAAAGAGAACGTTATCGTGGGTCGTCTGATCCCGGCAGGTACCGGTTACGCGTACCACTAGGa                                                                                             <  1:70915/100‑1 (MQ=255)
   agcCGTTGCGGGCAAACGCGACGAACTGCGCGGCCTGAAAGAGAACGTTATCGTGGGTCGTCTGATCCCGGCAGGTACCGGTTACGCGTACCACTAGGAt                                                                                            >  2:531345/1‑100 (MQ=255)
   agcCGTTGCGGGCAAACGCGACGAACTGCGCGGCCTGAAAGAGAACGTTATCGTGGGTCGTCTGATCCCGGCAGGTACCGGTTACGCGTACCACTAGGAt                                                                                            <  1:329267/100‑1 (MQ=255)
    gcCGTTGCGGGCAAACGCGACGAACTGCGCGGCCTGAAAGAGAACGTTATCGTGGGTCGTCTGATCCCGGCAGGTACCGGTTACGCGTACCACTAGGATc                                                                                           >  2:819904/1‑100 (MQ=255)
    gcCGTTGCGGGCAAACGCGACGAACTGCGCGGCCTGAAAGAGAACGTTATCGTGGGTCGTCTGATCCCGGCAGGTACCGGTTACGCGTACCACTAGGATc                                                                                           >  2:366889/1‑100 (MQ=255)
     ccGTTGCGGGCAAACGCGACGAACTGCGCGGCCTGAAAGAGAACGTTATCGTGGGTCGTCTGATCCCGGCAGGTACCGGTTACGCGTACCACTAGGATCg                                                                                          <  1:1061224/100‑1 (MQ=255)
      cGTTGCGGGCAAACGCGACGAACTGCGCGGCCTGAAAGAGAACGTTATCGTGGGTCGTCTGATCCCGGCAGGTACCGGTTACGCGTACCACTAGGATCg                                                                                          >  2:1481138/1‑99 (MQ=255)
       gTTGCGGGCAAACGCGACGAACTGCGCGGCCTGAAAGAGAACGTTATCGTGGGTCGTCTGATCCCGGCAGGTACCGGTTACGCGTACCACTAGGATCGTa                                                                                        >  1:250465/1‑100 (MQ=255)
         tGCGGGCAAACGCGACGAACTGCGCGGCCTGAAAGAGATCGTTATCGTGGGTCGTCTGTTCCCGGCAGGTACCGGTTACGCGTACCACTAGGATCGTATg                                                                                      <  1:873537/100‑1 (MQ=255)
           cGGGCAAACGCGACGAACTGCGCGGCCTGAAAGAGAACGTTATCGTGGGTCGTCTGATCCCGGCAGGTACCGGTTACGCGTATCACTAGGATCGTATGCg                                                                                    <  1:273783/100‑1 (MQ=255)
           cGGGCAAACGCGACGAACTGCGCGGCCTGAAAGAGAACGTTATCGTGGGTCGTCTGATCCCGGCAGGTACCGGTTACGCGTACCACTAGGATCGTATGCg                                                                                    <  1:939510/100‑1 (MQ=255)
           cGGGCAAACGCGACGAACTGCGCGGCCTGAAAGAGAACGTTATCGTGGGTCGTCTGATCCCGGCAGGTACCGGTTACGCGTACCACTAGGATCGTATGCg                                                                                    >  2:830693/1‑100 (MQ=255)
             ggCAAACGCGACGAACTGCGCGGCCTGAAAGAGAACGTTATCGTGGGTCGTCTGATCCCGGCAGGTACCGGCTACGCGTACCACTAGGATCGTATGCGTc                                                                                  >  1:959614/1‑100 (MQ=255)
               cAAACGCGACGAACTGCGCGGCCTGAAAGAAAACGTTATCGTGGGTCGTCTGATCCCGGCAGGTACCGGTTACGCGTACCACTAGGATCGTATGCGTCGc                                                                                >  1:1048341/1‑100 (MQ=255)
                    gcgACGAACTGCGCGGCCTGAAAGAGAACGTTATCGTGTGTCGTCTGATCCCGGCAGGTACCGGTTACGCGTACCACTAGGATCGTATGCATCGCCGt                                                                             >  2:675857/1‑98 (MQ=255)
                     cgacgaACTGCGCGGCCTGAAAGAGAACGTTATCGTGGGTCGTCTGATCCCGGCAGGTACCGGTTACGCGTACCACTAGGATCGTATGCGTCGCCGtgct                                                                          <  2:39705/100‑1 (MQ=255)
                      gacgaACTGCGCGGCCTGAAAGAGAACGTTATCGTGGGTCGTCTGATCCCGGCAGGTACCGGTTACGCGTACCACTAGGATCGTATGCGTCGCCGtgctg                                                                         <  1:1361263/100‑1 (MQ=255)
                            cTGCGCGGCCTGAAAGAGAACGTTATCGTGGGTCGTCTGATCCCGGCAGGTACCGGTTACGCGTACCACTAGGATCGTATGCGTCGCCGTGCTGCGGGTg                                                                   >  2:1247949/1‑100 (MQ=255)
                              gcgcGGCCTGAAAGAGAACGTTATCGGGGGTCGTCTGATCCCGGCAGGTACCGGTTACGCGTACCACTAGGATCGTATGCGTCGCCGTGCTGCGGGTGa                                                                  <  1:203087/99‑1 (MQ=255)
                                gcgGCCTGAAAGAGAACGTTATCGTGGGTCGTCTGATCCCGGCAGGTACCGGTTACGCGTACCACTAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAg                                                                <  1:1369045/99‑1 (MQ=255)
                                 cgGCCTGAAAGAGAACGTTATCGTGGGTCGTCTGATCCCGGCAGGTACCGGTTACGCGTACCACTAGGATCGTATGCGTCGCCGTGCTGCggtgcagccg                                                              >  1:1289612/1‑92 (MQ=255)
                                   gCCTGAAAGAGAACGTTATCGTGGGTCGTCTGATCCCGGCAGGTACCGGTTACGCGTACCACTAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTcc                                                            >  2:357611/1‑100 (MQ=255)
                                    ccTGAAAGAGAACGTTATCGTGGGTCGTCTGATCCCGGCAGGTACCGGTTACGCGTACCACTAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCg                                                           >  1:1528993/1‑100 (MQ=255)
                                     cTGAAAGAGAACGTTATCGTGGGTCGTCTGATCCCGGCAGGTACCGGTTACGCGTACCACTAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCgg                                                          >  1:1166572/1‑100 (MQ=255)
                                      tGAAAGAGAACGTTATCGTGGGTCGTCTGATCCCGGCAGGTACCGGTTACGCGTACCACTAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGc                                                         >  2:929604/1‑100 (MQ=255)
                                       gAAAGAGAACGTTATCGTGGGTGGTCTGATCCCGGCAGGTACCGGTTACGCGTACCACTAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGCt                                                        >  1:927038/1‑100 (MQ=255)
                                       gAAAGAGAACGTTATCGTGGGTCGTCTGATCCCGGCAGGTACCGGTTACGCGTACCACTAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGCt                                                        >  1:649370/1‑100 (MQ=255)
                                         aaGAGAACGTTATCGTGGGTCGTCTGATCCCGGCAGGTACCGGTTACGCGTACCACTAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGCTGc                                                      <  2:174292/100‑1 (MQ=255)
                                          agagAACGTTATCGTGGGTCGTCTGATCCCGGCAGGTACCGGTTACGCGTACCACTAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGCTGCa                                                     <  2:907022/100‑1 (MQ=255)
                                          agagAACGTTATCGTGGGTCGTCTGATCCCGGCAGGTACCGGTTACGCGTACCACTAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGCTGCa                                                     <  1:1481594/100‑1 (MQ=255)
                                           gagaACGTTATCGTGGGTCGTCTGATCCCGGCAGGTACCGGTTACGCGTACCACTAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGCTGc                                                      <  1:451497/98‑1 (MQ=255)
                                           gagaACGTTATCGTGGGTCGTCTGATCCCGGCAGGTACCGGTTACGCGTACCACTAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGCTGCAc                                                    >  2:5717/1‑100 (MQ=255)
                                               aCGTTATCGTGGGTCGTCTGATCCCGGCAGGTACCGGTTACGCGTACCACTAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGCTGCACCGCa                                                <  2:253883/100‑1 (MQ=255)
                                                 gTTATCGTGGGTCGTCTGATCCCGGCAGGTACCGTTTACGCGTACCACTAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGCTGCACCGCAgg                                              <  1:844694/100‑1 (MQ=255)
                                                 gTTATCGTGGGTCGTCTGATCCCGGCAGGTACCGGTTACGCGTACCACTAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGCTGCACCGCAgg                                              <  1:725881/100‑1 (MQ=255)
                                                   tATCGTGGGTCGTCTGATCCCGGCAGGTCCCGGTTACGCGTACCACGAGGATCGTATGCGTCGCCGTGCTGCGGGTGAATCGCCGGCTGCACCGCAGGtn                                            <  1:975755/100‑2 (MQ=255)
                                                   tATCGTGGGTCGTCTGATCCCGGCAGGTACCGGTTACGCGTACCACTAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGCTGCACCGCAGGTg                                            <  2:1048351/100‑1 (MQ=255)
                                                     tCGTGGGTCGTCTGATCCCGGCAGGTACCGGTTACGCGTACCACTAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGCTGCACCGCAGGTGAc                                          <  1:142810/100‑1 (MQ=255)
                                                       gTGGGTCGTCTGATCCCGGCAGGTACCGGTTACGCGTACCACTAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGCTGCACCGCAGGTGACTg                                        <  1:357608/100‑1 (MQ=255)
                                                         gggTCGTCTGATCCCGGCAGGTACCGGTTACGCGTACCACTAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGCTGCACCGCAGGTGACTGCa                                      >  2:168652/1‑100 (MQ=255)
                                                           gtcgtcTGATCCCGGCAGGTACCGGTTACGCGTACCACTAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGCTGCACCGCAGGTGACTGCaga                                    <  2:576740/100‑1 (MQ=255)
                                                            tcgtcTGATCCCGGCAGGTACCGGTTACGCGTACCACTAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGCTGCACCGCAGGTGACTGCagaa                                   <  1:531341/100‑1 (MQ=255)
                                                              gtcTGATCCCGGCAGGTACCGGTTACGCGTACCACTAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGCTGCACCGCAGGTGACTGCagaaga                                 >  1:1099787/1‑100 (MQ=255)
                                                              gtcTGATCCCGGCAGGTACCGGTTACGCGTACCACTAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGCTGCACCGCAGGTGACTGCagaaga                                 >  1:1099792/1‑100 (MQ=255)
                                                                 tGATCCCGGCAGGTACCGGTTACGCGTACCACTAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGCTGCACCGCAGGTGACTGCAGAAGACGc                              <  2:244648/100‑1 (MQ=255)
                                                                      ccGGCAGGTACCGGTTACGCGTACCACTAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGCTGCACCGCAGGTGACTGCAGAAGACGCATCTg                         >  1:1415846/1‑100 (MQ=255)
                                                                           aGGTACCGGTTACGCGTACCACTAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGCTGCACCGCAGGTGACTGCAGAAGACGCATCTGCCAGc                    <  2:1381050/100‑1 (MQ=255)
                                                                            ggTACCGGTTACGCGTACCACTAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGCTGCACCGCAGGTGACTGCAGAAGACGCATCTGCCAGcc                   <  2:492737/100‑1 (MQ=255)
                                                                             gTACCGGTTACGCGTACCACTAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGCTGCACCGCAGGTGACTGCAGAAGACGCATCTGCCAGCCt                  <  1:848605/100‑1 (MQ=255)
                                                                              tACCGGTTACGCGTACCACTAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGCTGCACCGCAGGTGACTGCAGAAGACGCATCTGCCAGCCTg                 <  1:1239455/100‑1 (MQ=255)
                                                                              tACCGGTTACGCGTACCACTAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGCTGCACCGCAGGTGACTGCAGAAGACGCATCTGCCAGCCTg                 >  1:178759/1‑100 (MQ=255)
                                                                                ccGGTTACGCGTACCACTAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGCTGCACCGCAGGTGACTGCAGAAGACGCATCTGCCAGCCTGGc               >  2:497345/1‑100 (MQ=255)
                                                                                ccGGTTACGCGTACCACTAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGCTGCACCGCAGGTGACTGCAGAAGACGCATCTGCCAGCCTGGc               <  2:185747/100‑1 (MQ=255)
                                                                                 cGGTTACGCGTACCACTAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGCTGCACCGCAGGTGACTGCAGAAGACGCATCTGCCAGGCTGGCa              <  1:1431218/100‑1 (MQ=255)
                                                                                  ggTTACGCGTACCACTAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGCTGCACCGCAGGTTACTGCAGAAGACGCATCTGCCAGCCTGGCAg             >  1:530710/1‑100 (MQ=255)
                                                                                  ggTTACGCGTACCACTAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGCTGCACCGCAGGTGACTGCAGAAGACGCATCTGCCAGCCTGGCAg             >  1:122897/1‑100 (MQ=255)
                                                                                     tACGCGTACCACTAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGCTGCACCGCAGGTGACTGCAGAAGACGCATCTGCCAGCCTGGCAGAAc          <  2:1096471/100‑1 (MQ=255)
                                                                                      aCGCGTACCACTAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGCTGCACCGCAGGTGACTGCAGAAGACGCATCTGCCAGCCTGGCAGAAct         <  1:124943/100‑1 (MQ=255)
                                                                                      aCGCGTACCACTAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGCTGCACCGCAGGTGACTGCAGAAGACGCATCTGCCAGCCTGGCAGAAct         <  1:1476074/100‑1 (MQ=255)
                                                                                       cgcgTACCACTAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGCTGCACCGCAGGTGACTGCAGAAGACGCATCTGCCAGCCTGGCAGAActg        <  1:254728/100‑1 (MQ=255)
                                                                                       cgcgTACCACTAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGCTGCACCGCAGGTGACTGCAGAAGACGCATCTGCCAGCCTGGCAGAActg        >  2:843804/1‑100 (MQ=255)
                                                                                         cgTACCACTAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGCTGCACCGCAGGTGACTGCAGAAGACGCATCTGCCAGCCTGGCAGAActgct      >  2:694307/1‑100 (MQ=255)
                                                                                         cgTACCACTAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGCTGCACCGCAGGTGACTGCAGAAGACGCATCTGCCAGCCTGGCAGAActgct      <  1:1470714/100‑1 (MQ=255)
                                                                                          gTACCACTAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGCTGCACCGCAGGTGACTGCAGAAGACGCATCTGCCAGCCTGGCAGAActgctg     >  2:922324/1‑100 (MQ=255)
                                                                                            accactAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGCTGCACCGCAGGTGACTGCAGAAGACGCATCTGCCAGCCTGGCAGAACTGCTGaa   <  2:1166586/100‑1 (MQ=255)
                                                                                             ccactaGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGCTGCACCGCAGGTGACTGCAGAAGACGCATCTGCCAGCCTGGCAGAACTGCTGAAc  <  1:1247935/100‑1 (MQ=255)
                                                                                                 |                                                                                               
AGCAGCCGTTGCGGGCAAACGCGACGAACTGCGCGGCCTGAAAGAGAACGTTATCGTGGGTCGTCTGATCCCGGCAGGTACCGGTTACGCGTACCACCAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGCTGCACCGCAGGTGACTGCAGAAGACGCATCTGCCAGCCTGGCAGAACTGCTGAAC  >  NC_000913/4189351‑4189543

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A