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
A8 F1 I2 R1 765 53.2 2691310 93.4% 2513683 103.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,159,054 Δ1 bp coding (565/918 nt) oxyR → oxidative and nitrosative stress transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,159,0510G.100.0% 291.1 / NA 68coding (562/918 nt)oxyRoxidative and nitrosative stress transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base . (35/33);  total (35/33)

GCGAAGCATTCATTGAAGTGCCGTTGTTTGATGAGCCAATGTTGCTGGCTATCTATGAAGATCACCCGTGGGCGAACCGCGAATGCGTACCGATGGCCGATCTGGCAGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGG  >  NC_000913/4158944‑4159183
                                                                                                           |                                                                                                                                    
gCGAAGCATTCATTGAAGTGCCGTTGTTTGATGAGCCAATGTTGCTGGCTATCTATGAAGATCACCCGTGGGCGAACCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCAc                                                                                                      >  1:1268772/1‑139 (MQ=255)
 cGAAGCATTCATTGAAGTGCCGTTGTTTGATGAGCCAATGTTGCTGGCTATCTATGAAGATCACCCGTGGGCGAACCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACt                                                                                                     >  2:115961/1‑139 (MQ=255)
            ttGAAGTGCCGTTGTTTGATGAGCCAATGTTGCTGGCTATCTATGAAGATCACCCGTGGGCGAACCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGAt                                                                                          <  1:1217390/139‑1 (MQ=255)
             tGAAGTGCCGTTGTTTGATGAGCCAATGTTGCTGGCTATCTATGAAGATCACCCGTGGGCGAACCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCCATc                                                                                         >  2:1277469/1‑139 (MQ=255)
               aaGTGCCGTTGTTTGATGAGCCAATGTTGCTGGCTATCTATGAAGATCACCCGTGGGCGAACCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATg                                                                                                                     <  2:298554/109‑1 (MQ=255)
               aaGTGCCGTTGTTTGATGAGCCAATGTTGCTGGCTATCTATGAAGATCACCCGTGGGCGAACCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATg                                                                                                                     >  1:298554/1‑109 (MQ=255)
                  tGCCGTTGTTTGATGAGCCAATGTTGCTGGCTATCTATGAAGATCACCCGTGGGCGAACCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCa                                                                                    <  2:845705/139‑1 (MQ=255)
                  tGCCGTTGTTTGATGAGCCAATGTTGCTGGCTATCTATGAAGATCACCCGTGGGCGAACCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCa                                                                                    <  1:612758/139‑1 (MQ=255)
                    ccGTTGTTTGATGAGCCAATGTTGCTGGCTATCTATGAAGATCACCCGTGGGCGAACCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGa                                                                                                                       <  1:1043291/102‑1 (MQ=255)
                    ccGTTGTTTGATGAGCCAATGTTGCTGGCTATCTATGAAGATCACCCGTGGGCGAACCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGa                                                                                                                       >  2:1043291/1‑102 (MQ=255)
                     cGTTGTTTGATGAGCCAATGTTGCTGGCTATCTATGAAGATCACCCGTGGGCGAACCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAActgctg                                                                                                                        >  1:1253108/1‑100 (MQ=255)
                     cGTTGTTTGATGAGCCAATGTTGCTGGCTATCTATGAAGATCACCCGTGGGCGAACCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAActgctg                                                                                                                        <  2:1253108/100‑1 (MQ=255)
                                   ccAATGTTGCTGGCTATCTATGAAGATCACCCGTGGGCGAACCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTc                                                                                                        >  1:146711/1‑102 (MQ=255)
                                   ccAATGTTGCTGGCTATCTATGAAGATCACCCGTGGGCGAACCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTc                                                                                                        <  2:146711/102‑1 (MQ=255)
                                   ccAATGTTGCTGGCTATCTATGAAGATCACCCGTGGGCGAACCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGa                                                                   >  2:189222/1‑139 (MQ=255)
                                    cAATGTTGCTGGCTATCTATGAAGATCACCCGTGGGCGAACCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCaa                                                                                   <  1:1160142/122‑1 (MQ=255)
                                    cAATGTTGCTGGCTATCTATGAAGATCACCCGTGGGCGAACCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCaa                                                                                   >  2:1160142/1‑122 (MQ=255)
                                    cAATGTTGCTGGCTATCTATG‑AGATCACCCGTGGGCGAACCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAActgct                                                                                                                         <  2:634619/83‑1 (MQ=255)
                                    cAATGTTGCTGGCTATCTATG‑AGATCACCCGTGGGCGAACCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAActgct                                                                                                                         >  1:634619/1‑83 (MQ=255)
                                            cTGGCTAGCTATGAAGATCACCCGTGGGCGAACCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTATCTGTTTTGAAGCCGGGGc                                                          >  2:880680/1‑139 (MQ=255)
                                                 tatctatGAAGATCACCCGTGGGCGAACCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATg                                                     <  1:269515/139‑1 (MQ=255)
                                                         aaGATCACCCGTGGGCGAACCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATaca                                             >  2:401017/1‑139 (MQ=255)
                                                             tCACCCGTGGGCGAACCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACt                                         >  2:952439/1‑139 (MQ=255)
                                                             tCACCCGTGGGCGAACCGCGAATGCGTACCGATGG‑‑GATCTGGCA‑GGGAAAACCTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGt                                                                              <  2:1119106/100‑1 (MQ=255)
                                                             tCACCCGTGGGCGAACCGCGAATGCGTACCGATGG‑‑GATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGt                                                                              >  1:1119106/1‑100 (MQ=255)
                                                              cACCCGTGGGCGAACCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTgg                                                                                                                 >  1:1254317/1‑66 (MQ=255)
                                                              cACCCGTGGGCGAACCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTgg                                                                                                                 <  2:1254317/66‑1 (MQ=255)
                                                               aCCCGTGGGCGAACCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAActgct                                                                                                                         >  2:863705/1‑57 (MQ=255)
                                                               aCCCGTGGGCGAACCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAActgct                                                                                                                         <  1:863705/57‑1 (MQ=255)
                                                               aCCCGTGGGCGAACCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGttt                                                                                                 >  1:224232/1‑81 (MQ=255)
                                                               aCCCGTGGGCGAACCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGttt                                                                                                 <  2:224232/81‑1 (MQ=255)
                                                               aCCCGTGGGCGAACCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGAt                                                                                          <  1:390528/88‑1 (MQ=255)
                                                               aCCCGTGGGCGAACCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGAt                                                                                          >  2:390528/1‑88 (MQ=255)
                                                               aCCCGTGGGCGAACCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGa                                                       <  2:1299576/123‑1 (MQ=255)
                                                               aCCCGTGGGCGAACCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGa                                                       >  1:1299576/1‑123 (MQ=255)
                                                                    tGGGCGAACCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTgg                                                                                                                 <  2:18112/60‑1 (MQ=255)
                                                                    tGGGCGAACCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTgg                                                                                                                 >  1:18112/1‑60 (MQ=255)
                                                                     gggCGAACCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCcgcgcg                                 >  2:607760/1‑139 (MQ=255)
                                                                       gCGAACCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGAc                               <  2:1268772/139‑1 (MQ=255)
                                                                        cGAACCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCgggg                                                           >  1:718299/1‑110 (MQ=255)
                                                                        cGAACCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCgggg                                                           <  2:718299/110‑1 (MQ=255)
                                                                        cGAACCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGAcc                              <  1:607760/139‑1 (MQ=255)
                                                                        cGAACCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGAcc                              <  2:156318/139‑1 (MQ=255)
                                                                          aaCCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAg                            >  2:39785/1‑139 (MQ=255)
                                                                          aaCCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAg                            <  1:39785/139‑1 (MQ=255)
                                                                           aCCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCgggg                                                           >  1:1253451/1‑107 (MQ=255)
                                                                           aCCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCgggg                                                           <  2:1253451/107‑1 (MQ=255)
                                                                           aCCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGc                           >  1:338331/1‑139 (MQ=255)
                                                                           aCCGCGAATGCGTACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGc                           >  2:123136/1‑139 (MQ=255)
                                                                                   tGCGTACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAAc                   <  1:880680/139‑1 (MQ=255)
                                                                                       tACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCgggg                                                           >  1:792019/1‑95 (MQ=255)
                                                                                       tACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCgggg                                                           <  2:468660/95‑1 (MQ=255)
                                                                                       tACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCgggg                                                           >  1:468660/1‑95 (MQ=255)
                                                                                       tACCGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCgggg                                                           <  2:792019/95‑1 (MQ=255)
                                                                                         ccGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTgcg             <  1:115961/139‑1 (MQ=255)
                                                                                         ccGATGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTgcg             <  1:401017/139‑1 (MQ=255)
                                                                                            aTGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGt                                                                                                         >  2:1237232/1‑44 (MQ=255)
                                                                                            aTGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGt                                                                                                         <  1:1237232/44‑1 (MQ=38)
                                                                                             tGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCaa          <  2:1009112/138‑1 (MQ=255)
                                                                                             tGGCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCaa          >  1:1009112/1‑138 (MQ=255)
                                                                                              ggCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGa                                                    <  2:1206052/95‑1 (MQ=255)
                                                                                              ggCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGa                                                    >  1:1206052/1‑95 (MQ=255)
                                                                                              ggCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATaca                                             >  2:708057/1‑102 (MQ=255)
                                                                                              ggCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATaca                                             <  1:708057/102‑1 (MQ=255)
                                                                                               gCCGATCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACAt       >  1:753895/1‑139 (MQ=255)
                                                                                                    tCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCgggg                                                           <  2:695406/82‑1 (MQ=255)
                                                                                                    tCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCgggg                                                           >  1:695406/1‑82 (MQ=255)
                                                                                                    tCTGGCA‑GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACAtggtgg  >  2:937513/1‑139 (MQ=255)
                                                                                                           |                                                                                                                                    
GCGAAGCATTCATTGAAGTGCCGTTGTTTGATGAGCCAATGTTGCTGGCTATCTATGAAGATCACCCGTGGGCGAACCGCGAATGCGTACCGATGGCCGATCTGGCAGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGG  >  NC_000913/4158944‑4159183

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