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 F60 I1 R1 15 82.6 2828648 98.9% 2797532 138.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,091,492 A→T L292Q (CTG→CAG)  frvB ← putative PTS enzyme IIBC component FrvB

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,091,4920AT98.2% 179.8 / NA 55L292Q (CTG→CAG) frvBputative PTS enzyme IIBC component FrvB
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base T (25/29);  minor base G (1/0);  total (26/29)
Fisher's exact test for biased strand distribution p-value = 4.73e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTTTCCAGCAGTGAGAAGCAGAAGAACCAGGCGGTTTTATTGATGGGGCCGCCCATATCGAACGCCAGCATCGCACCGACCAGAAACGCTGCCGCAAACTTCATTGATGGAGGAATGGTATTCAGGAAGTGGAGCAGCCCGCCCATGAGGTCGGACATCACCGGCCCGATAACGTAGTAAGTGAGCACGCCGAAAACCAGCAGAGTAACGAACGGGATCAGCATTGAACCGAGCAGCGGTTGTAATGCTTTGCCAAGGCGCACTTTGCGGA  >  NC_000913/4091357‑4091627
                                                                                                                                       |                                                                                                                                       
ttttCCAGCAGTGAGAAGCAGAAGTACCAGGCGGTTTTATTGATGGGGCCGCCCATATCGAACGCCAGCATCGCACCGACCAGAAACGCTGCCGCAAACTTCATTGATGGAGGAATGGTATTCAGGAAGTGGAGCTgccc                                                                                                                                     >  2:963535/1‑140 (MQ=255)
  ttCCAGCAGTGAGAAGCAGAAGAACCAGGCGGTTTTATTGATGGGGCCGCCCATATCGAACGCCAGCATCGCACCGACCAGAAACGCTGCCGCAAACTTCATGGATGGAGGAATGGTGTTCAGGGAGTGGAGCTgcccgc                                                                                                                                   >  1:410855/1‑140 (MQ=255)
      agcagTGAGAAGCAGAAGAACCAGGCGGTTTTATTGATGGGGCCGCCCATATCGAACGCCAGCATCGCACCGACCAGAAACGCTGCCGCAAACTTCATTGATGGAGGAATGGTATTCAGGAAGTGGAGCTGCCCGCCCAt                                                                                                                               <  1:896003/140‑1 (MQ=255)
                  cAGAAGAACCAGGCGGTTTTATTGATGGGGCCGCCCATATCGAACGCCAGCATCGCACCGACCAGAAACGCTGCCGCAAACTTCATTGATGGAGGAATGGTATTCAGGAAGTGGAGCTGCCCGCCCATGAGGTCGGACAt                                                                                                                   >  1:1139540/1‑140 (MQ=255)
                     aagaaCCAGGCGGTTTTATTGATGGGGCCGCCCATATCGAACGCCAGCATCGCACCGACCAGAAACGCTGCCGCAAACTTCATTGATGGAGGAATGGTATTCTGGAAGTGCAGCGGCGCGCCCATGAGGTCGGACATCAc                                                                                                                >  1:615056/1‑140 (MQ=255)
                             ggCGGTTTTATTGATGGGGCCGCCCATATCGAACGCCAGCATCGCACCGACCAGAAACGCTGCCGCAAACTTCATTGATGGAGGAATGGGAATCAGGAAGAGGAACTGCCCGCCCATCAGGTCGGACATCACCGGCCCGa                                                                                                        >  2:518988/1‑140 (MQ=255)
                              gCGGTTTTATTGATGGGGCCGCCCATATCGAACGCCAGCATCGCACCGACCAGAAACGCTGCCGCAAACTTCATTGATGGAGGAATGGTATTCAGGAAGTGGAGCTGCCCGCCCATGAGGTCGGACATCACCGGCCCGAt                                                                                                       <  1:241731/140‑1 (MQ=255)
                              gCGGTTTTATTGATGGGACCGCCCATATCGAACGCCAGCCTCGCACCGTCCAGAAACGCTGCCGCAAACTTCATTGATGGAGGAATGGTATTCAGGAAGTGGAGCTGCCCGCCCATGAGGTCGGACATCACCGGCCCGAt                                                                                                       <  2:410855/140‑1 (MQ=255)
                                ggTTTTATTGATGGGGCCGCCCATATCGAACGCCAGCATCGCACCGACCAGAAACGCTGCCGCAAACTTCATTGATGGAGGAATGGTATTCAGGAAGTGGAGCTGCCCGCCCATGAGGTCGGACATCACCGGCCCGATaa                                                                                                     <  1:963535/140‑1 (MQ=255)
                                   tttATTGATGGGGCCGCCCATATCGGACGGCAGCATCTCACCGACCAGAAACGCTGCCGCAAACTTCATTGATGGAGGAATGGTATTCAGGAAGTGGAGCTGCCCGCCCATGAGGTCGGACATCACCGGCCCGATAACgt                                                                                                  <  1:518988/140‑1 (MQ=255)
                                    ttATTGATGGGGCCGCCCATATCGAACGCCAGCATCGCACCGACCAGAAACGCTGCCGCAAACTTCATTGATGGAGGAATGGTATTCAGGAAGTGGAGCTGCCCGCCCATGAGGTCGGACATCACCGGCCCGATAACgta                                                                                                 <  1:1367878/140‑1 (MQ=255)
                                            ggggCCGCCCATATCGAACGCCAGCATCGCACCGACCAGAAACGCTGCCGCAAACTTCATTGATGGAGGAATGGTATTCAGGAAGTGGAGCTGCCCGCCCATGAGGTCGGACATCACCGGCCCGAt                                                                                                       <  1:1036015/126‑1 (MQ=255)
                                            ggggCCGCCCATATCGAACGCCAGCATCGCACCGACCAGAAACGCTGCCGCAAACTTCATTGATGGAGGAATGGTATTCAGGAAGTGGAGCTGCCCGCCCATGAGGTCGGACATCACCGGCCCGAt                                                                                                       >  2:1036015/1‑126 (MQ=255)
                                            ggggCCGCCCATATCGAACGCCAGCATCGCACCGACCAGAAACGCTGCCGCAAACTTCATTGATGGAGGAATGGTATTCAGGAAGTGGAGCTGCCCGCCCATGAGGTCGGACATCACAGGCCCGATAACGTAGTAAGTGa                                                                                         >  2:533350/1‑140 (MQ=255)
                                               gccgccCATATCGAACGCCAGCATCGAACCGACCAGAAACGCTGCCGCAAACTTCATTGATGGAGGAATGGTATTCAGGAAGTGGAGCTGCCCGCCCATGAGGTCGGACATCACCGGCCCGATAACGTAGTAAGTGAGCa                                                                                      >  2:315152/1‑140 (MQ=255)
                                                         tCGAACGCCAGCATCGCACCGACCAGAAACGCTGCCGCAAACTTCATTGATGGAGGAATGGTATTCAGGAAGTGGAGCTGCCCGCCCATGAGGTCGGACATCACCGGCCCGATAACGTAGTAAGTGAGCACGCCGAAAAc                                                                            <  1:918987/140‑1 (MQ=255)
                                                            aaCGCCAGCATCGCATCGACCAGAAACGCGGCCGCAACCTTCATTGATGGAGGAATGGTATTCAGGAAGTGGAGCTGCCCGCCCATGAGGTCGGACATCACCGGCCCGATAACGTAGTAAGTGAGCACGCCGAAAACcag                                                                         <  1:621694/140‑1 (MQ=255)
                                                            aaCGCCAGCATCGCACCGACCAGAATCGCTGCCGCAATCTTCATTGATGGAGGAATGGTATTCAGGAAGTGGAGCTGCCCGCCCATGAGGTCGGACATCACCGGCCCGATAACGTAGTAAGTGAGCACGCCGAAAACcag                                                                         <  1:460292/140‑1 (MQ=255)
                                                            aaCGCCAGCATCGCACCGACCAGAAACGCTGCCGCAAACTTCATTGATGGAGGAATGGTATTCAGGAAGTGGAGCTGCCCGCCCATGAGGTCGGACATCACCGGCCCGATAACGTAGTAAGTGAGCACGCCGAAAACcag                                                                         <  2:11884/140‑1 (MQ=255)
                                                            aaCGCCAGCATCGCACCGACCAGAAACGCTGCCGCAAACTTCATTGATGGAGGAATGGTATTCAGGAAGTGGAGCTGCCCGCCCATGAGGTCGGACATCACCGGCCCGATAACGTAGTAAGTGAGCACGCCGAAAACcag                                                                         <  1:735446/140‑1 (MQ=255)
                                                            aaCGCCAGCATCGCACCCACCAGAAACGCTGCCACAAACTTCATTGATTGAGGAATGGTATTCAGGAAGTGGAGCTGCCCGCCCATGAGGTCGGACATCACCGGCCCGATAACGTAGTAAGTGAGCACGCCGAAAACcag                                                                         <  2:615056/140‑1 (MQ=255)
                                                             aCGCCAGCATCGCACCGACCAGAAACGCTGCCGCAAACTTCATTGATGGAGGAATGGTATTCAGGAAGTGGAGCTGCCCGCCCATGAGGTCGGACATCACCGGCCCGATAACGTAGTAAGTGAGCACGCCGAAAACca                                                                          <  2:1016763/138‑1 (MQ=255)
                                                             aCGCCAGCATCGCACCGACCAGAAACGCTGCCGCAAACTTCATTGATGGAGGAATGGTATTCAGGAAGTGGAGCTGCCCGCCCATGAGGTCGGACATCACCGGCCCGATAACGTAGTAAGTGAGCACGCCGAAAACca                                                                          >  1:1016763/1‑138 (MQ=255)
                                                                  aGCATCGCACCGACCAGAAACGCTGCCGCAAACTTCATTGATGGAGGAATGGTATTCAGGAAGTGGAGCTGCCCGCCCATGAGGTCGGACATCACCGGCCCGATAACGTAGTAAGTGAGCACGCCGAAAACCAGCAGAGt                                                                   >  2:781344/1‑140 (MQ=255)
                                                                         cACCGACCAGAAACGCTGCCGCCAAATTCCTTGATGGCGGAATGGTATTCAGGAAGTGGAGCTGCCCGCCCATGAGGTCGGACATCACCGGCCCGATAACGTAGTAAGTGAGCACGCCGAAAACCAGCAGAGTaacgaac                                                            <  1:383870/140‑1 (MQ=255)
                                                                         cACCGACCAGAAACGCTGCCGCAAACTTCATTGATGGAGGAATGGTATTCAGGAAGTGGAGCTGCCCGCCCATGAGGTCGGACATCACCGGCCCGATAACGTAGTAAGTGAGCACGCCGAAAACCAGCAGAGTaacgaac                                                            >  2:818319/1‑140 (MQ=255)
                                                                              aCCAGAAACGCTGCCGCAAACTTCATTGATGGAGGAATGGTATTCAGGAAGTGGAGCTGCCCGCCCATGAGGTCGGACATCACCGGCCCGATAACGTAGTAAGTGAGCACGCCGAAAACCAGCAGAGTAACGAACGGGAt                                                       <  1:818319/140‑1 (MQ=255)
                                                                              aCCAGAAACGCTGCCGCAAACTTCATTGATGGAGGAATGGTATTCAGGAAGTGGAGCTGCCCGCCCATGAGGTCGGACATCACCGGCCCGATAACGTAGTAAGTGAGCACGCCGAAAACCAGCAGAGTAACGAACGGGAt                                                       <  1:1162935/140‑1 (MQ=255)
                                                                              aCCAGAAACGCTGCCGCAAACTTCACTGAGGGAGGAATGGTATTCAGGAAGTGGAGCTGCCCGCCCATGAGGTCGGACATCACCGGCCCGATAACGTAGTAAGTGAGCACGCCGAAAACCAGCAGAGTAACGAACGGGAt                                                       <  1:596934/140‑1 (MQ=255)
                                                                                   aaaCGCTGCCGCAAACTTCATTGATGGAGGAATGGTATTCAGGAAGTGGAGCTGCCCGCCCATGAGGTCGGACATCACCGGCCCGATAACGTAGTAAGTGAGCACGCCGAAAACCAGCAGAGTaacgaac                                                            <  1:1317925/130‑1 (MQ=255)
                                                                                   aaaCGCTGCCGCAAACTTCATTGATGGAGGAATGGTATTCAGGAAGTGGAGCTGCCCGCCCATGAGGTCGGACATCACCGGCCCGATAACGTAGTAAGTGAGCACGCCGAAAACCAGCAGAGTaacgaac                                                            >  2:1317925/1‑130 (MQ=255)
                                                                                        cTGCCGCAAACTTCATTGATGGAGGAATGGTATTCAGGAAGTGGAGCTGCCCGCCCATGAGGTCGGACATCACCGGCCCGATAACGTAGTAAGTGAGCACGCCGAAAACCAGCAGAGTaacgaa                                                             >  2:763495/1‑124 (MQ=255)
                                                                                        cTGCCGCAAACTTCATTGATGGAGGAATGGTATTCAGGAAGTGGAGCTGCCCGCCCATGAGGTCGGACATCACCGGCCCGATAACGTAGTAAGTGAGCACGCCGAAAACCAGCAGAGTaacgaa                                                             <  1:763495/124‑1 (MQ=255)
                                                                                              cAAACTTCATTGATGTAGGAATTGTTTTCAGGAAGTGTAGCTGCCCGCGCATGAGGTCGGACATCACCGGCTCGATAACGTAGTAAGTGAGCGCGCCGAAACCCAGCAGAGTAACGAACGGGATCAGCATTGAACCGagc                                       <  1:533350/140‑1 (MQ=255)
                                                                                              cAAACTTCATTGATGGAGGAATGGTATTCAGGAAGTGGAGCTGCCCGCCCATGAGGTCGGACATCACCGGCCCGATAACGTAGTAAGTGAGCACGCCGAAAACCAGCAGAGTAACGAACGGGATCAGCATTGAACCGagc                                       <  2:1139540/140‑1 (MQ=255)
                                                                                                     cATTGATGGAGGAATGGTATTCAGGAAGTGGAGCTGCCCGCCCATGAGGTCGGACATCACCGGCCCGATAACGTAGTAAGTGAGCACGCCGAAAACCAGCTGAGTAACCAACGGGATCAGCACTGAACCGAGCAGCGGtt                                >  2:534756/1‑140 (MQ=255)
                                                                                                     cATTGATGGAGGAATGGTATTCAGGAAGTGGAGCTGCCCGCCCATGAGGTCGGACATCACCGGCCCGATAACGTAGTAAGTGAGCACGCCGAAAACCAGCAGAGTAACGAACGGGATCAGCATTGAAc                                            >  1:1057569/1‑128 (MQ=255)
                                                                                                     cATTGATGGAGGAATGGTATTCAGGAAGTGGAGCTGCCCGCCCATGAGGTCGGACATCACCGGCCCGATAACGTAGTAAGTGAGCACGCCGAAAACCAGCAGAGTAACGAACGGGATCAGCATTGAAc                                            <  2:1057569/128‑1 (MQ=255)
                                                                                                     cATTGATGGAGGAATGGTATTCAGGAAGTGGAGCTGCCCGCCCATGAGGTCGGACATCACCGGCCCGATAACGTAGTAAGTGAGCACGCCGAAAACCAGCAGAGTAACGAACGGGATCAGCATTGAACCGagcagc                                    <  2:1049758/136‑1 (MQ=255)
                                                                                                     cATTGATGGAGGAATGGTATTCAGGAAGTGGAGCTGCCCGCCCATGAGGTCGGACATCACCGGCCCGATAACGTAGTAAGTGAGCACGCCGAAAACCAGCAGAGTAACGAACGGGATCAGCATTGAACCGagcagc                                    >  1:1049758/1‑136 (MQ=255)
                                                                                                     cATTGATGGAGGAATGGTATTCAGGAAGTGGAGCTGCCCGCCCATGAGGTCGGACATCACCGGCCCGATAACGTAGTAAGTGAGCACGCCGAAAACCAGCAGAGTAACGAACGGGATCAGCATTGAACCGagcagc                                    >  2:1171863/1‑136 (MQ=255)
                                                                                                     cATTGATGGAGGAATGGTATTCAGGAAGTGGAGCTGCCCGCCCATGAGGTCGGACATCACCGGCCCGATAACGTAGTAAGTGAGCACGCCGAAAACCAGCAGAGTAACGAACGGGATCAGCATTGAACCGagcagc                                    <  1:1171863/136‑1 (MQ=255)
                                                                                                     cATTGATGGAGGAATGGTATTCAGGAAGTGGAGCTGCCCGCCCATGAGGTCGGACATCACCGGCCCGATAACGTAGTAAGTGAGCACGCCGAAAACCAGCAGAGTAACGAACGGGATCAGCATTGAACCGAGCAGCGGtt                                >  1:1243742/1‑140 (MQ=255)
                                                                                                            ggaggaATGGTATTCAGGAAGTGGAGCTGCCCGCCCATGAGGTCGGACATCACCGGCCCGATAACGTAGTAAGTGAGCACGCCGAAAACCAGCAGAGTAACGAACGGGATCAGCATTGAACCGAGCAGCGGTTGTAATGc                         >  1:823200/1‑140 (MQ=255)
                                                                                                             gagggATGGTATTCAGGAAGTGGAGCTGCCCGCCCATGAGGTCGGACATCACCGGCCCGATAACGTAGTAAGTGAGCACGCCGAAAACCAGCAGAGTAACGAACGGGATCAGCATTGAACCGAGCAGCGGTTGTAATGCt                        >  1:333508/1‑140 (MQ=255)
                                                                                                             gaggaATGGTATTCAGGAAGTGGAGCTGCCCGCCCATGAGGt                                                                                                                          >  2:945225/1‑42 (MQ=255)
                                                                                                             gaggaATGGTATTCAGGAAGTGGAGCTGCCCGCCCATGAGGt                                                                                                                          <  1:945225/42‑1 (MQ=255)
                                                                                                                        ttCAGGAAGTGGAGCTGCCCGCCCATGAGGTCGGACATCACCGGCCCGATAACGTAGTAAGTGAGCACGCCGAAAACCAGCAGAGTAACGAACGGGATCAGCATTGAACCGAGCAGCTGTTGTAATGCTTTGCCAAGgcg             >  1:480017/1‑140 (MQ=255)
                                                                                                                        ttCAGGAAGTGGAGCTGCCCGCCCATGAGGTCGGACATCACCGGCCCGATAACGTAGTAAGTGAGCACGCCGAAAACCAGCAGAGTAACGAACGGGATCAGCATTGAACCGAGCAGCGGTTGTAATGCTTTGCCAAGgcg             <  1:781344/140‑1 (MQ=255)
                                                                                                                        ttCAGGAAGTGGAGCTGCCCGCCCATGAGGTCGGACATCACCGGCCCGATAACGTAGTAAGTGAGCACGCCGAAAACCAGCAGAGTAACGAACGGGATCAGCATTGAACCGAGCAGCGGTTGTAATGCCTTGCCAAGgcg             >  1:235201/1‑140 (MQ=255)
                                                                                                                           aGGAAGTGGAGCTGCTCGCCCATGACGTCGGACATCAACGGCCCGATAACGTAGTAAGTGAGCACGCCGAAAACCAGCAGAGTAACGAACGGGATCAGCATTGAACCGAGCAGCGGTTGTAATGCTTTGCCAAGGCGCAc          <  1:647465/140‑1 (MQ=255)
                                                                                                                             gAAGTGGAGCTGCCCGCCCATGAGGTCGGACATCACCGGCCCGATAACGTAGTAAGTGAGCACGCCGAAAACCAGCAGAGTAACGAACGGGATCAGCATTGAACCGAGCAGCGGTTGTAATGCTTTGCCAAGGCGCACtt        >  2:1153045/1‑140 (MQ=255)
                                                                                                                             gAAGTGGAGCTGCCCGCCCATGAGGTCGGACATCACCGGCCCGATAACGTAGTAAGTGAGCACGCCGAAAACCAGCAGAGTAACGAACGGGATCAGCATTGAACCGAGCAGCGGGTGCAATGCTGTGCCAAGGCGCACtt        >  1:610244/1‑140 (MQ=255)
                                                                                                                               aGTGGAGCTGCCCGCCTGTGAGTTCGGACATTACCGGCCCGATAACGTCGTAAGTGAGCACGCCGAAAACCAGCAGAGTAACGAACGGGATCAGCATTGAACCGAGCAGCGGTTGTAATGCTTTGCCAAGGCGCACTTTg      <  2:610244/140‑1 (MQ=255)
                                                                                                                                gTGGAGCTGCCCGCCCATGAGGTCGGACATCACCGGCCCGATAACGTAGTAAGTGAGCACGCCGAAAACCAGCAGAGTAACGAACGGGATCAGCATTGAACCGAGCAGCGGTTGTAATGCTTTGCCAAGGCGCACTTTGc     >  1:134281/1‑140 (MQ=255)
                                                                                                                                  ggAGCTGCCCGCCCATGAGGTCGGACATCACCGGCCCGATAACGTAGTAAGTGAGCACGCCGAAAACCAGCAGAGTAACGAACGGGATCAGCATTGAACCGAGCAGCGGTTGTAATGCCTTGCCAAGGCGCACTTTGCgg   <  2:235201/140‑1 (MQ=255)
                                                                                                                                   gAGCTGCCCGCCCATGAGGTCGGACATCACCGGCCCGATAACGTAGTAAGTGAGCACGCCGAAAACCAGCAGAGTAACGAACGGGATCAGCATTGAACCGAGCAGCGGTTGTAATGCTTTGCCAAGGCGCACTTTGCGGa  >  1:1257545/1‑140 (MQ=255)
                                                                                                                                       |                                                                                                                                       
TTTTCCAGCAGTGAGAAGCAGAAGAACCAGGCGGTTTTATTGATGGGGCCGCCCATATCGAACGCCAGCATCGCACCGACCAGAAACGCTGCCGCAAACTTCATTGATGGAGGAATGGTATTCAGGAAGTGGAGCAGCCCGCCCATGAGGTCGGACATCACCGGCCCGATAACGTAGTAAGTGAGCACGCCGAAAACCAGCAGAGTAACGAACGGGATCAGCATTGAACCGAGCAGCGGTTGTAATGCTTTGCCAAGGCGCACTTTGCGGA  >  NC_000913/4091357‑4091627

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A