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
A12 F1 I1 R1 760 58.2 3022526 90.8% 2744453 102.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,691,192 G→A Q447Q (CAG→CAA)  ydgA → DUF945 family protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,691,1920GA98.2% 178.7 / NA 56Q447Q (CAG→CAA) ydgADUF945 family protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (24/31);  minor base T (0/1);  total (24/32)
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

CTGACCATTCCGGTGGATATGGCAACTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCAGATGTTCCGTCTGACCACCTTGCAGGACAATACCATCACCACCAGCCTGCAATATGCTAACGGTCAGATAACGTTAAATGGGCAGAAAATGTCGTTAGAAGATTTTGTTGGCATGTTTGCGATG  >  NC_000913/1691067‑1691315
                                                                                                                             |                                                                                                                           
cTGACCATTCCGGTGGATATGGCAACTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCAAATGTTCCGTCTGa                                                                                                                <  1:916761/139‑1 (MQ=255)
cTGACCATTCCGGTGGATATGGCAACTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCAAATGTTCCGTCTGa                                                                                                                <  1:909029/139‑1 (MQ=255)
cTGACCATTCCCGTGGATATGGCAACTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCAAATGTTCCGTCTGa                                                                                                                <  1:983426/139‑1 (MQ=255)
   aCCATTCCGGTGGATATGGCAACTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTAGAAGGTGCATCAGCAATGGGGCAAATGTTCCGTCTGacca                                                                                                             <  1:917563/139‑1 (MQ=255)
      aTTCCGGTGGATATGGCAACTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCAAATGTTCCGTCTGACCACCt                                                                                                          <  2:952775/139‑1 (MQ=255)
             tGGATATGGCAACTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCAAATGTTCCGTCTGACCACCTTGCAGGa                                                                                                   <  1:1090460/139‑1 (MQ=255)
               gATATGGCAACTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCAAATGTTCCGTCTGACCACCTTGCAGGACa                                                                                                 >  2:1129102/1‑139 (MQ=255)
                 tatGGCAACTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCAAATGTTCCGTCTGACCACCTTGCAGGACAAt                                                                                               >  2:457586/1‑139 (MQ=255)
                 tatGGCAACTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCAAATGTTCCGTCTGACCACCTTGCAGGACAAt                                                                                               <  2:1229291/139‑1 (MQ=255)
                          tGAGTTTATGACTCAGGTAGCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCAAATGTTCCGTCTGACCACCTTGCAGGACAATACCATcacc                                                                                      >  1:35115/1‑139 (MQ=255)
                           gAGTTTATGACTCAGGTAGCGAAGCTGGAAGGTTATCAGGAAGATCAAGCTAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCAAATGTTCCGTCTGACCACCTTGCAGGACAATACCATcacca                                                                                     <  1:955421/139‑1 (MQ=255)
                            aGTTTATGACTCAGGTAGCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCAAATGTTCCGTCTGACCACCTTGCAGGACAATACCATcaccac                                                                                    <  2:517324/139‑1 (MQ=255)
                              tttATGACTCAGGTAGCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCAAATGTTCCGTCTGACCACCTTGCAGGACAATACCATCAccacca                                                                                  <  1:1129102/139‑1 (MQ=255)
                                 aTGACTCAGGTAGCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCAAATGTTCCGTCTGACCACCTTg                                                                                                        >  1:675819/1‑114 (MQ=255)
                                 aTGACTCAGGTAGCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCAAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCAAATGTTCCGTCTGACCACCTTg                                                                                                        <  2:675819/114‑1 (MQ=255)
                                    aCTCAGGTAGCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCAAATg                                                                                                                          <  2:728542/93‑1 (MQ=255)
                                    aCTCAGGTAGCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCAAATg                                                                                                                          >  1:728542/1‑93 (MQ=255)
                                      tCAGGTAGCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCAAATGTTCCGTCTGa                                                                                                                <  2:771910/101‑1 (MQ=255)
                                      tCAGGTAGCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCAAATGTTCCGTCTGa                                                                                                                >  1:771910/1‑101 (MQ=255)
                                       cAGGTAGCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCAAATGTTCCGTCTGACCACCTTGCAGGAc                                                                                                  >  2:1045916/1‑114 (MQ=255)
                                       cAGGTAGCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCAAATGTTCCGTCTGACCACCTTGCAGGAc                                                                                                  <  1:1045916/114‑1 (MQ=255)
                                        aGGTAGCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCAAATGTTCCGTCTGACCACCTTg                                                                                                        <  2:300777/107‑1 (MQ=255)
                                        aGGTAGCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCAAATGTTCCGTCTGACCACCTTg                                                                                                        >  1:300777/1‑107 (MQ=255)
                                            aGCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCAAATGTTCCGTCTGACCACCTTGCAGGACAATACCATCACCACCAGCCTGCAATATGCt                                                                    <  2:952413/139‑1 (MQ=255)
                                              tataagagacaGGTTATCAGGAAGATCAAGCGAAAAACCTGGCCAAACAGCCAGTTGAAGGTGCATCAGCCATGGGGCATATGTTCCGTCTGCCCACCTTGCAGGACAATCCCATCACCACCAGCCTGCAATATGCTaa                                                                  <  2:454053/129‑1 (MQ=255)
                                              cGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCAAATGTTCCGTCTGACCACCTTGCAGGACAATACCATCACCACCAGCCTGCAATATGCTaa                                                                  <  2:35115/139‑1 (MQ=255)
                                                aaGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCAAATGTTCCGTCTGACCACCTTGCAGGACAATACCATCACCACCAGc                                                                                <  1:684094/123‑1 (MQ=255)
                                                aaGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCAAATGTTCCGTCTGACCACCTTGCAGGACAATACCATCACCACCAGc                                                                                >  2:684094/1‑123 (MQ=255)
                                                    tGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCAAATGTTCCGTCTGa                                                                                                                <  2:1034519/87‑1 (MQ=255)
                                                    tGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCAAATGTTCCGTCTGa                                                                                                                >  1:1034519/1‑87 (MQ=255)
                                                      gAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCAAATGTTCCGTCTGACCACCTTGCAGGACAATACCATcaccac                                                                                    <  1:1078776/113‑1 (MQ=255)
                                                      gAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCAAATGTACCGTCTGACCACCTTGCAGGACAATACCATcaccac                                                                                    >  2:1078776/1‑113 (MQ=255)
                                                              tCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCAAATGTTCCGTCTGacca                                                                                                             <  1:551298/80‑1 (MQ=255)
                                                              tCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCAAATGTTCCGTCTGacca                                                                                                             >  2:551298/1‑80 (MQ=255)
                                                                     gATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCAAATGTTCCGTCTGACCACCTTGCAGGACAATACCATCACCACCAGCCTGCAATATGCTAACGGTCAGATAActgtctcttata                                           >  1:454053/1‑128 (MQ=255)
                                                                     gATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGAATCAGCAATGGGGCAAATGTTCCGTCTGACCACCTTGCAGGACAATACCATCACCACCAGCCTGCAATATGCTAACGGt                                                              <  1:970487/120‑1 (MQ=255)
                                                                     gATAAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCAAATGTTCCGTCTGACCACCTTGCAGGACAATACCATCTCCACCAGCCTGCAATATGCTAACGGt                                                              >  2:970487/1‑120 (MQ=255)
                                                                          aGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCAAATGTTCCGTCTGACCACCTTGCAGGACAATACCATCACCACCAGCCTGCAATATGCt                                                                    <  2:1324447/109‑1 (MQ=255)
                                                                          aGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCAAATGTTCCGTCTGACCACCTTGCAGGACAATACCATCACCACCAGCCTGCAATATGCt                                                                    >  1:1324447/1‑109 (MQ=255)
                                                                            cGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCAAATGTTc                                                                                                                       >  2:700038/1‑56 (MQ=255)
                                                                            cGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCAAATGTTc                                                                                                                       <  1:700038/56‑1 (MQ=255)
                                                                                aaaaCTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCAAATATTCCGTCTGACCACCTTGCAGGACAATACCATCACCACCAGCCTGCAATATGCTAACGGTCAGa                                                          >  2:138934/1‑113 (MQ=255)
                                                                                aaaaCTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCAAATATTCCGTCTGACCACCTTGCAGGACAATACCATCACCACCAGCCTGCAATATGCTAACGGTCAGa                                                          <  1:138934/113‑1 (MQ=255)
                                                                                        cGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCAAATGTTCCGTCTGACCACCTTGCAGGACAATACCATCACCACCAGCCTGCAATATGCTAACGGTCAGATAACGTTAAATGGGCAGAAAATGTCGTTagaaga                        >  2:329152/1‑139 (MQ=255)
                                                                                         gAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCAAATGTTCCGTCTGACCACCTTGCAGGACAATACCATcacca                                                                                     >  2:1036904/1‑77 (MQ=255)
                                                                                         gAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCAAATGTTCCGTCTGACCACCTTGCAGGACAATACCATcacca                                                                                     <  1:1036904/77‑1 (MQ=255)
                                                                                                    ttGAAGGTGCATCAGCAATGGGGCAAATGTTCCGTCTGACCACCTTGCAGGACAATACCATCACCACCAGCCTGCAATATGCTAACGGTCAGATAACGTTAAATGGGCAGAAAATGTCGTTAGAAGATTTTGTTGGCAt            <  1:329152/139‑1 (MQ=255)
                                                                                                              aTCAGCAATGGGGCAAATGTTCCGTCTGACCACCTTGCAGGACAATACCATCACCACCAGCCTGCAATATGCTAACGGTCAGATAACGTTAAATGGGCAGAAAATGt                                  >  2:1268459/1‑107 (MQ=255)
                                                                                                              aTCAGCAATGGGGCAAATGTTCCGTCTGACCACCTTGCAGGACAATACCATCACCACCAGCCTGCAATATGCTAACGGTCAGATAACGTTAAATGGGCAGAAAATGt                                  <  1:1268459/107‑1 (MQ=255)
                                                                                                              aTCAGCAATGGGGCAAATGTTCCGTCTGACCACCTTGCAGGACAATACCATCACCACCAGCCTGCAATATGCTAACGGTCAGATAACGTTAAATGGGCAGAAAATGTCGTTAGAAGATTTTGTTGGCATGTTTGCGATg  >  1:432323/1‑139 (MQ=255)
                                                                                                                     aTGGGGCAAATGTTCCGTCTGACCACCTTGCAGGACAATACCATCACCACCAGCCTGCAATATGCTAACGGTCAGa                                                          <  2:434540/76‑1 (MQ=255)
                                                                                                                     aTGGGGCAAATGTTCCGTCTGACCACCTTGCAGGACAATACCATCACCACCAGCCTGCAATATGCTAACGGTCAGa                                                          >  1:434540/1‑76 (MQ=255)
                                                                                                                      tGGGGCAAATGTTCCGTCTGACCACCTTGCAGGACAATACCATCACCACCAGCCTGCAATATGCt                                                                    >  2:999780/1‑65 (MQ=255)
                                                                                                                      tGGGGCAAATGTTCCGTCTGACCACCTTGCAGGACAATACCATCACCACCAGCCTGCAATATGCt                                                                    <  1:999780/65‑1 (MQ=255)
                                                                                                                        gggCAAATGTTCCGTCTGACCACCTTGCAGGACaa                                                                                                >  2:1446845/1‑35 (MQ=255)
                                                                                                                        gggCAAATGTTCCGTCTGACCACCTTGCAGGACaa                                                                                                <  1:1446845/35‑1 (MQ=255)
                                                                                                                             |                                                                                                                           
CTGACCATTCCGGTGGATATGGCAACTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCAGATGTTCCGTCTGACCACCTTGCAGGACAATACCATCACCACCAGCCTGCAATATGCTAACGGTCAGATAACGTTAAATGGGCAGAAAATGTCGTTAGAAGATTTTGTTGGCATGTTTGCGATG  >  NC_000913/1691067‑1691315

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A