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 F28 I1 R1 227 52.0 1764248 99.3% 1751898 138.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,956,094 T→C Q305R (CAG→CGG)  torZ ← trimethylamine N‑oxide reductase 2

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,956,0940TC98.2% 201.6 / ‑4.0 57Q305R (CAG→CGG) torZtrimethylamine N‑oxide reductase 2
Reads supporting (aligned to +/- strand):  ref base T (0/0);  major base C (24/32);  minor base A (0/1);  total (24/33)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.86e-01

CCATCAGCATTGTGCGATTCGCCGCCATCAGTTCAGCGAGTTTGACTATCTGCGCTTCCGGTACGCCAGTAATTTCCGCCGCCCAGACCGCGCTCTTCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACTGCGGATACCCGGTAGTGTATTTTTCAAGGAACACTTTATCGTGTTTGCCTTGTGTCATCAGGGTATGCGCAATCCCTAACATCAGTGCCACGTCGGTGCCCATATTCGGCGCGATCCAGGTGGCATTATCGTCA  >  NC_000913/1955957‑1956228
                                                                                                                                         |                                                                                                                                      
ccATCAGCATTGTGCGATTCGCCGCCATCAGTTCAGCGAGTTTGACTATCTGCGCTTCCGGTACGCCAGTAATTTCCGCCGCCCAGACCGCGCTCTTCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACCGc                                                                                                                                      <  2:422330/140‑1 (MQ=255)
ccATCAGCATTGTGCGATTCGCCGCCATCAGTTCAGCGAGTTTGACTATCTGCGCTTCCGGTACGCCAGTAATTTCCGCCGCCCAGACCGCGCTCTTCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACCGc                                                                                                                                      >  2:454339/1‑140 (MQ=255)
  aTCAGCATTGTGCGATTCGCCGCCATCAGTTCAGCGAGTTTGACTATCTGCGCTTCCGGTACGCCAGTAATTTCCGCCGCCCAGACCGCGCTCTTCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACCGCgg                                                                                                                                    <  2:848980/140‑1 (MQ=255)
      gCATTGTGCGATTCGCCGCCATCAGTTCAGCGAGTTTGACTATCTGCGCTTCCGGTACGCCAGTAATTTCCGCCGCCCAGACCGCGCTCTTCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACCGCGGATAc                                                                                                                                >  1:600747/1‑140 (MQ=255)
      gCATTGTGCGATTCGCCGCCATCAGTTCAGCGAGTTTGACTATCTGCGCTTCCGGTACGCCAGTAATTTCCGCCGCCCAGACCGCGCTCTTCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACCGCGGATAc                                                                                                                                >  2:751388/1‑140 (MQ=255)
       cATTGTGCGATTCGCCGCCATCAGTTCAGCGAGTTTGACTATCTGCGCTTCCGGTACGCCAGTAATTTCCGCCGCCCAGACCGCGCTCTTCGGCGTATTATCGCTCTTTCCTGTCAGATACTCTTCAAACCGCGGATAcc                                                                                                                               <  1:506051/140‑1 (MQ=255)
       cATTGTGCGATTCGCCGCCATCAGTTCAGCGAGTTTGACTATCTGCGCTTCCGGTACGCCAGTAATTTCCGCCGCCCAGACCGCGCTCTTCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACCGCGGATAcc                                                                                                                               <  1:777314/140‑1 (MQ=255)
       cATTGTGCGATTCGCCGCCATCAGTTCAGCGAGTTTGACTATCTGCGCTTCCGGTACGCCAGTAATTTCCGCCGCCCAGACCGCGCTCTTCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACAGCGGATAcc                                                                                                                               <  2:286849/140‑1 (MQ=255)
          tgtgCGATTCGCCGCCATCAGTTCAGCGAGTTTGACTATCTGCGCTTCCGGTACGCCAGTAATTTCCGCCGCCCAGACCGCGCTCTTCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACCGCgg                                                                                                                                    <  1:566937/132‑1 (MQ=255)
          tgtgCGATTCGCCGCCATCAGTTCAGCGAGTTTGACTATCTGCGCTTCCGGTACGCCAGTAATTTCCGCCGCCCAGACCGCGCTCTTCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACCGCgg                                                                                                                                    >  2:566937/1‑132 (MQ=255)
          tgtgCGATTCGCCGCCATCAGTTCAGCGAGTTTGACTATCTGCGCTTCCGGTACGCCAGTAATTTCCGCCGCCCAGACCGCGCTCTTCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACCGCGGATACCCgg                                                                                                                            >  2:561730/1‑140 (MQ=255)
          tgtgCGATTCGCCGCCATCAGTTCAGCGAGTTTGACTATCTGCGCTTCCGGTACGCCAGTAATTTCCGCCGCCCAGACCGCGCTCTTCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACCGCGGATACCCgg                                                                                                                            >  1:403419/1‑140 (MQ=255)
                 ttCGCCGCCATCAGTTCAGCGAGTTTGACTATCTGCGCTTCCGGTACGCCAGTAATTTCCGCCGCCCAGACCGCGCTCTTCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACCGCGGATACCCGGTAGTGTa                                                                                                                     <  1:195483/140‑1 (MQ=255)
                 ttCGCCGCCATCAGTTCAGCGAGTTTGACTATCTGCGCTTCCGGTACGCCAGTAATTTCCGCCGCCCAGACCGCGCTCTTCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACCGCGGATACCCGGTAGTGTa                                                                                                                     <  2:304403/140‑1 (MQ=255)
                        ccATCAGTTCAGCGAGTTTGACTATCTGCGCTTCCGGTACGCCAGTAATTTCCGCCGCCCAGACCGCGCTCTTCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACCGCGGATACCCGGTAGTGTATTTTTCa                                                                                                              <  1:751388/140‑1 (MQ=255)
                        ccATCAGTTCAGCGAGTTTGACTATCTGCGCTTCCGGTACGCCAGTAATTTCCGCCGCCCAGACCGCGCTCTTCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACCGCGGATACCCGGTAGTGTATTTTTCa                                                                                                              <  1:227462/140‑1 (MQ=255)
                          aTCAGTTCAGCGAGTTTGACTATCTGCGCTTCCGGTACGCCAGTAATTTCCGCCGCCCAGACCGCGCTCTTCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACCGCGGATACCCGGTAGTGTATTTTTCAAg                                                                                                            <  2:403419/140‑1 (MQ=255)
                          aTCAGTTCAGCGAGTTTGACTATCTGCGCTTCCGGTACGCCAGTAATTTCCGCCGCCCAGACCGCGCTCTTCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACCGCGGATACCCGGTAGTGTATTTTTCAAg                                                                                                            <  2:212477/140‑1 (MQ=255)
                                 cAGCGAGTTTGACTATCTGCGCTTCCGGTACGCCAGTAATTTCCGCCGCCCAGACCGCGCTCTTCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACCGCGGATACCCGGTAGTGTATTTTTCAAGGAACACt                                                                                                     <  1:26043/140‑1 (MQ=255)
                                  aGCGAGTTTGACTATCTGCGCTTCCGGTACGCCAGTAATTTCCGCCGCCCAGACCGCGCTCTTCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACCGCGGATACCCGGTAGTGTATTTTTCAAGGAACACtt                                                                                                    >  2:444227/1‑140 (MQ=255)
                                    cGAGTTTGACTATCTGCGCTTCCGGTACGCCAGTAATTTCCGCCGCCCAGACCGCGCTCTTCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACCGCGGATACCCGGTAGTGTATTTTTCAAGGAACACTTTa                                                                                                  <  1:360122/140‑1 (MQ=255)
                                    cGAGTTTGACTATCTGCGCTTCCGGTACGCCAGTAATTTCCGCCGCCCAGACCGCGCTCTTCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACCGCGGATACCCGGTAGTGTATTTTTCAAGGAACACTTTa                                                                                                  >  2:264604/1‑140 (MQ=255)
                                         ttGACTATCTGCGCTTCCGGTACGCCAGTAATTTCCGCCGCCCAGACCGCGCTCTTCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACCGCGGATACCCGGTAGTGTATTTTTCAAGGAACACTTTATCgtg                                                                                             >  1:305171/1‑140 (MQ=255)
                                            aCTATCTGCGCTTCCGGTACGCCAGTAATTTCCGCCGCCCAGACCGCGCTCTTCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACCGCGGATACCCGGTAGTGTATTTTTCAAGGAACACTTTATCGTGttt                                                                                          <  1:49762/140‑1 (MQ=255)
                                              tATCTGCGCTTCCGGTACGCCAGTAATTTCCGCCGCCCAGACCGCGCTCTTCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACCGCGGATACCCGGTAGTGTATTTTTCAAGGAACACTTTATCGTGTTTGc                                                                                        <  1:312683/140‑1 (MQ=255)
                                              tATCTGCGCTTCCGGTACGCCAGTAATTTCCGCCGCCCAGACCGCGCTCTTCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACCGCGGATACCCGGTAGTGTATTTTTCAAGGAACACTTTATCGTGTTTGc                                                                                        <  2:533113/140‑1 (MQ=255)
                                               aTCTGCGCTTCCGGTACGCCAGTAATTTCCGCCGCCCAGACCGCGCTCTTCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACCGCGGATACCCGGTAGTGTATTTTTCAAGGAACACTTTATCGTGTTTGcc                                                                                       <  2:438669/140‑1 (MQ=255)
                                                  tGCGCTTCCGGTACGCCAGTAATTTCCGCCGCCCAGACCGCGCTCTTCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACCGCGGATACCCGGTAGTGTATTTTTCAAGGAACACTTTATCGTGTTTGCCTtg                                                                                    <  2:438624/140‑1 (MQ=255)
                                                   gcgcTTCCGGTACACCAGTAATTTCCGCCGCCCAGACCGCGCTCTTCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACCGCGGATACCCGGTAGTGTATTTTTCAAGGAACACTTTATCGTGTTTGCCTtgt                                                                                   <  1:374726/140‑1 (MQ=255)
                                                    cgcTTCCGGTCCGCCAGTAATTTCCGCCGCCCAGACCGCGCTCTTCGGCGTATCATCGCTCATACCTGTCAGATACCATTCAAACCCAGCATACCCGGTAGTGTATTTTTCACGCAACAGTCTATCGTGTTTGCCTtgtg                                                                                  <  2:587468/140‑1 (MQ=255)
                                                    cgcTTCCGGTACGCCAGTAATTTCCGCCGCCCAGACCGCGCTCTTCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACCGCGGATACCCGGTAGTGTATTTTTCAAGGAACACTTTATCGTGTTTGCCTtgtg                                                                                  <  2:600747/140‑1 (MQ=255)
                                                         ccGGTACGCCAGTAATTTCCGCCGCCCAGACCGCGCTCTTCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACCGCGGATACCCGGTAGTGTATTTTTCAAGGAACACTTTATCGTGTTTGCCTTGTGtcatc                                                                             <  1:310817/140‑1 (MQ=255)
                                                          cGGTACGCCAGTAATTTCCGCCGCCCAGACCGCGCTCTTCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACCGCGGATACCCGGTAGTGTATTTTTCAAGGAACACTTTATCGTGTTTGCCTTGTGtcatca                                                                            >  2:166489/1‑140 (MQ=255)
                                                              aCGCCAGTAATTTCCGCCGCCCAGACCGCGCTCTTCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACCGCGGATACCCGGTAGTGTATTTTTCAAGGAACACTTTATCGTGTTTGCCTTGTGTCATCAGGGt                                                                        <  1:669836/140‑1 (MQ=255)
                                                                   aGTAATTTCCGCCGCCCAGACCGCGCTCTTCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACCGCGGATACCCGGTAGTGTATTTTTCAAGGAACACTTTATCGTGTTTGCCTTGTGTCATCAGGGTATgcg                                                                   >  2:481024/1‑140 (MQ=255)
                                                                    gTAATTTCCGCCGCCCAGACCGCGCTCTTCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACCGCGGATACCCGGTAGTGTATTTTTCAAGGAACACTTTATCGTGTTTGCCTTGTGTCATCAGGGTATgcgc                                                                  <  1:264604/140‑1 (MQ=255)
                                                                     tAATTTCCGCCGCCCAGACCGCGCTCTTCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACCGCGGATACCCGGTAGTGTATTTTTCAAGGAACACTTTATCGTGTTTGCCTTGTGTCATCAGGGTATGCGCa                                                                 <  1:561730/140‑1 (MQ=255)
                                                                     tAATTTCCGCCGCCCAGACCGCGCTCTTCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACCGCGGATACCCGGTAGTGTATTTTTCAAGGAACACTTTATCGTGTTTGCCTTGTGTCATCAGGGTATGCGCa                                                                 >  1:315244/1‑140 (MQ=255)
                                                                     tAATTTCCGCCGCCCAGACCGCGCTCTTCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACCGCGGATACCCGGTAGTGTATTTTTCAAGGAACACTTTATCGTGTTTGCCTTGTGTCATCAGGGTATGCGCa                                                                 <  1:166489/140‑1 (MQ=255)
                                                                            cgccgcCCAGACCGCGCTCTTCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACCGCGGATACCCGGTAGTGTATTTTTCAAGGAACACTTTATCGTGTTTGCCTTGTGTCATCAGGGTATGCGCAATCCCTa                                                          >  1:126920/1‑140 (MQ=255)
                                                                              ccgccCAGACCGCGCTCTTCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACCGCGGATACCCGGTAGTGTATTTTTCAAGGAACACTTTATCGTGTTTGCCTTGTGTCATCAGGGTATGCGCa                                                                 >  1:57129/1‑131 (MQ=255)
                                                                              ccgccCAGACCGCGCTCTTCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACCGCGGATACCCGGTAGTGTATTTTTCAAGGAACACTTTATCGTGTTTGCCTTGTGTCATCAGGGTATGCGCa                                                                 <  2:57129/131‑1 (MQ=255)
                                                                                 cccAGACCGCGCTCTTCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACCGCGGATACCCGGTAGTGTATTTTTCAAGGAACACTTTATCGTGTTTGCCTTGTGTCATCAGGGTATGCGCAATCCCTAACATc                                                     >  2:833567/1‑140 (MQ=255)
                                                                                             tctTCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACCGCGGATACCCGGTAGTGTATTTTTCAAGGAACACTTTATCGTGTTTGCCTTGTGTCATCAGGGTATGCGCAATCCCTAACATCAGTGCCACGTCg                                         <  1:833567/140‑1 (MQ=255)
                                                                                                tCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACCGCGGATACCCGGTAGTGTATTTTTCAAGGAACACTTTATCGTGTTTGCCTTGTGTCATCAGGGTATGCGCAATCCCTAACAt                                                      >  1:62447/1‑124 (MQ=255)
                                                                                                tCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACCGCGGATACCCGGTAGTGTATTTTTCAAGGAACACTTTATCGTGTTTGCCTTGTGTCATCAGGGTATGCGCAATCCCTAACAt                                                      <  2:62447/124‑1 (MQ=255)
                                                                                                         tatCGCTCTTACCTGTCAGATACTCTTCAAACCGCGGATACCCGGTAGTGTATTTTTCAAGGAACACTTTATCGTGTTTGCCTTGTGTCATCAGGGTATGCGCAATCCCTAACATCAGTGCCACGTCGGTGCCCATATTc                             >  2:231925/1‑140 (MQ=255)
                                                                                                           tCGCTCTTACCTGTCAGATACTCTTCAAACCGCGGATACCCGGTAGTGTATTTTTCAAGGAACACTTTATCGTGTTTGCCTTGTGTCATCAGGGTATGCGCAATCCCTAACATCAGTGCCACGTCGGTGCCCATATTCgg                           >  1:584887/1‑140 (MQ=255)
                                                                                                           tCGCTCTTACCTGTCAGATACTCTTCAAACCGCGGATACCCGGTAGTGTATTTTTCAAGGAACACTTTATCGTGTTTGCCTTGTGTCATCAGGGTATGCGCAATCCCTAACATCAGTGCCACGTCGGTGCCCATATTCgg                           >  1:460784/1‑140 (MQ=255)
                                                                                                             gCTCTTACCTGTCAGATACTCTTCAAACCGCGGATACCCGGTAGTGTATTTTTCAAGGAACACTTTATCGTGTTTGCCTTGTGTCATCAGGGTATGCGCAATCCCTAACATCAGTGCCACGTCGGTGCCCATATTCGgcg                         <  1:481024/140‑1 (MQ=255)
                                                                                                             gCTCTTACCTGTCAGATACTCTTCAAACCGCGGATACCCGGTAGTGTATTTTTCAAGGAACACTTTATCGTGTTTGCCTTGTGTCATCAGGGTATGCGCAATCCCTAACATCAGTGCCACGTCGGTGCCCATATTCGgcg                         <  1:454339/140‑1 (MQ=255)
                                                                                                              ctctTACCTGTCAGATACTCTTCAAACCGCGGATACCCGGTAGTGTATTTTTCAAGGAACACTTTATCGTGTTTGCCTTGTGTCATCAGGGTATGCGCAATCCCTAACATCAGTGCCACGTCgg                                        <  2:859343/124‑1 (MQ=255)
                                                                                                              ctctTACCTGTCAGATACTCTTCAAACCGCGGATACCCGGTAGTGTATTTTTCAAGGAACACTTTATCGTGTTTGCCTTGTGTCATCAGGGTATGCGCAATCCCTAACATCAGTGCCACGTCgg                                        >  1:859343/1‑124 (MQ=255)
                                                                                                                               ctctTCAAACCGCGGATACCCGGTAGTGTATTTTTCAAGGAACACTTTATCGTGTTTGCCTTGTGTCATCAGGGTATGCGCAATCCCTAACATCAGTGCCACGTCGGTGCCCATATTCGGCGCGATCCAGGTGGCATTAt       >  1:163283/1‑140 (MQ=255)
                                                                                                                                tctTCAAACCGCGGATACCCGGTAGTGTATTTTTCAAGGAACACTTTATCGTGTTTGCCTTGTGTCATCAGGGTATGCGCAATCCCTAACATCAGTGCCACGTCGGTGCCCATATTCGGCGCGATCCAGGTGGCATTATc      >  2:679449/1‑140 (MQ=255)
                                                                                                                                  ttCAAACCGCGGATACCCGGTAGTGTATTTTTCAAGGAACACTTTATCGTGTTTGCCTTGTGTCATCAGGGTATGCGCAATCCCTAACATCAGTGCCACGTCGGTGCCCATATTCGGCGCGATCCAGGTGGCATTATCGt    >  2:653061/1‑140 (MQ=255)
                                                                                                                                  ttCAAACCGCGGATACCCGGTAGTGTATTTTTCAAGGAACACTTTATCGTGTTTGCCTTGTGTCATCAGGGTATGCGCAATCCCTAACATCAGTGCCACGTCGGTGCCCATATTCGGCGCGATCCAGGTGGCATTATCGt    >  2:566144/1‑140 (MQ=255)
                                                                                                                                    cAAACCGCGGATACCCGGTAGTGTATTTTTCAAGGAACACTTTATCGTGTTTGCCTTGTGTCATCAGGGTATGCGCAATCCCTAACATCAGTGCCACGTCGGTGCCCATATTCGGCGCGATCCAGGTGGCATTATCGTCa  <  1:444227/140‑1 (MQ=255)
                                                                                                                                         |                                                                                                                                      
CCATCAGCATTGTGCGATTCGCCGCCATCAGTTCAGCGAGTTTGACTATCTGCGCTTCCGGTACGCCAGTAATTTCCGCCGCCCAGACCGCGCTCTTCGGCGTATTATCGCTCTTACCTGTCAGATACTCTTCAAACTGCGGATACCCGGTAGTGTATTTTTCAAGGAACACTTTATCGTGTTTGCCTTGTGTCATCAGGGTATGCGCAATCCCTAACATCAGTGCCACGTCGGTGCCCATATTCGGCGCGATCCAGGTGGCATTATCGTCA  >  NC_000913/1955957‑1956228

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A