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
A1 F1 I2 R1 765 46.1 2269152 93.8% 2128464 105.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,484,897 (C)6→7 coding (524/3594 nt) evgS → hybrid sensory histidine kinase in two‑component regulatory system with EvgA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,484,8911.C96.2% 172.8 / ‑0.2 53coding (518/3594 nt)evgShybrid sensory histidine kinase in two‑component regulatory system with EvgA
Reads supporting (aligned to +/- strand):  ref base . (2/0);  new base C (23/28);  total (25/28)
Fisher's exact test for biased strand distribution p-value = 2.18e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.81e-01

CGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑C‑C‑CCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTACTTTATTGGTAGTAACATCATTACCAG  >  NC_000913/2484756‑2485023
                                                                                                                                        |                                                                                                                                      
cgccgcCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑c‑c‑c                                                                                                                                   >  1:821363/1‑139 (MQ=255)
   cgccTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑c‑c‑cccc                                                                                                                                >  1:606917/1‑139 (MQ=255)
     ccTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑c‑c‑ccccca                                                                                                                              <  2:567746/139‑3 (MQ=255)
                      tgctgcAACCAAACCACTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGTGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACC‑C‑CCCCAGACGAGGTAATtcatca                                                                                                              >  1:977965/1‑139 (MQ=255)
                       gctgcAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACC‑C‑CCCCAGACGAGGTAATTCatcaa                                                                                                             >  1:126382/1‑139 (MQ=255)
                               caaaccaTTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACC‑C‑CCCCAGACGAGGTAATTCATCAATCATTTcc                                                                                                     <  2:263352/139‑1 (MQ=255)
                                        gATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACC‑C‑CCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGcaac                                                                                            >  1:34059/1‑139 (MQ=255)
                                                ccTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACC‑C‑CCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTAtct                                                                                    >  1:196894/1‑139 (MQ=255)
                                                   ttCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACC‑C‑CCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAAtt                                                                                        >  1:1015139/1‑132 (MQ=255)
                                                   ttCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACC‑C‑CCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAAtt                                                                                        <  2:1015139/132‑1 (MQ=255)
                                                    tCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACC‑C‑CCCCAGACGAGGTAATTCatcaatc                                                                                                           >  1:777708/1‑112 (MQ=255)
                                                    tCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACC‑C‑CCCCAGACGAGGTAATTCatcaatc                                                                                                           <  2:777708/112‑1 (MQ=255)
                                                    tCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACC‑C‑CCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCttt                                                                                >  2:408348/1‑139 (MQ=255)
                                                    tCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCATACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑c‑c‑cccccaga                                                                                                                            >  1:373478/1‑90 (MQ=255)
                                                    tCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCATACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑c‑c‑cccccaga                                                                                                                            <  2:373478/94‑5 (MQ=255)
                                                      cGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACC‑C‑CCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTa                                                                              <  2:126382/139‑1 (MQ=255)
                                                      cGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACC‑C‑CCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTa                                                                              <  2:34059/139‑1 (MQ=255)
                                                           cTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACC‑C‑CCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAAt                                                                         >  2:625853/1‑139 (MQ=255)
                                                           cTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACC‑C‑CCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAAt                                                                         >  1:1085031/1‑139 (MQ=255)
                                                                  ccaccCTTCACGACTCAATGTGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACC‑C‑CCCCAGACGAAGTAATTCATCAATCCTTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATc                                                                  <  2:977965/139‑1 (MQ=255)
                                                                     cccTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACC‑C‑CCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAgg                                                               <  2:1085031/139‑1 (MQ=255)
                                                                             gACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACC‑C‑CCCCAGACGAGGTAATTCATCAATCATTTCCa                                                                                                    <  1:99263/94‑1 (MQ=255)
                                                                             gACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACC‑C‑CCCCAGACGAGGTAATTCATCAATCATTTCCa                                                                                                    >  2:99263/1‑94 (MQ=255)
                                                                             gACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACC‑C‑CCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTatat                                                                   >  2:253770/1‑127 (MQ=255)
                                                                             gACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACC‑C‑CCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTatat                                                                   <  1:253770/127‑1 (MQ=255)
                                                                             gACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACC‑C‑CCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCa                                                       >  1:707179/1‑139 (MQ=255)
                                                                                tCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACC‑C‑CCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCa                                                       >  2:291399/1‑136 (MQ=255)
                                                                                tCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACC‑C‑CCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCa                                                       <  1:291399/136‑1 (MQ=255)
                                                                                    tGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACC‑C‑CCCCAGACGAGGTaa                                                                                                                     <  2:2919/70‑1 (MQ=255)
                                                                                    tGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACC‑C‑CCCCAGACGAGGTaa                                                                                                                     >  1:2919/1‑70 (MQ=255)
                                                                                            cTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACC‑C‑CCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATc                                                                  <  1:454685/113‑1 (MQ=255)
                                                                                            cTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACC‑C‑CCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATc                                                                  >  2:454685/1‑113 (MQ=255)
                                                                                                    aCCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACC‑C‑CCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGca                                      <  2:1038919/133‑1 (MQ=255)
                                                                                                    aCCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACC‑C‑CCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGa                                <  2:223241/139‑1 (MQ=255)
                                                                                                    aCCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑c‑c‑ccccca                                                                                                                              >  1:817272/1‑42 (MQ=255)
                                                                                                    aCCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑c‑c‑ccccca                                                                                                                              <  2:817272/44‑3 (MQ=255)
                                                                                                    aCCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑CTC‑CCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGca                                      >  1:1038919/1‑133 (MQ=255)
                                                                                                     ccAAAACCAGTAAATATTGCTCGGGTAGCAAATTACC‑C‑CCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGAt                               <  1:408348/139‑1 (MQ=255)
                                                                                                            cAGTAAATATTTCTCGGGTAGCAAATTACC‑C‑CCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGACACAATGATTACTTTa                        <  1:840311/139‑1 (MQ=255)
                                                                                                              gTAAATATTGCTCGGGTAGCAAATTACC‑C‑CCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGcaa                                                                                             <  2:703674/68‑1 (MQ=255)
                                                                                                              gTAAATATTGCTCGGGTAGCAAATTACC‑C‑CCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTACTTTAtt                      <  1:625853/139‑1 (MQ=255)
                                                                                                              gTAAATATTGCTCGGGTAGCAAATTA‑C‑CGCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGcaa                                                                                             >  1:703674/1‑68 (MQ=255)
                                                                                                                aaaTATTGCTCGGGTAGCAAATTACC‑C‑CCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTAc                            >  2:184444/1‑131 (MQ=255)
                                                                                                                aaaTATTGCTCGGGTAGCAAATTACC‑C‑CCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTAc                            <  1:184444/131‑1 (MQ=255)
                                                                                                                    atTGCTCGGGTAGCAAATTACC‑C‑CCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTACTTTATTGgtagt                <  2:821363/139‑1 (MQ=255)
                                                                                                                     ttGCTCGGGTAGCAAATTACC‑C‑CCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTACTTTATTGgtagta               <  2:707179/139‑1 (MQ=255)
                                                                                                                      tGCTCGGGTAGCAAATTACC‑C‑CCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTACTTTATTGGTAGTaa              >  2:1090604/1‑139 (MQ=255)
                                                                                                                       gCTCGGGTAGCAAATTACC‑C‑CCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTatat                                                                   <  2:234369/85‑1 (MQ=255)
                                                                                                                       gCTCGGGTAGCAAATTACC‑C‑CCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTatat                                                                   >  1:234369/1‑85 (MQ=255)
                                                                                                                        cTCGGGTAGCAAATTACC‑C‑CCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGcac                                     >  1:625471/1‑114 (MQ=255)
                                                                                                                        cTCGGGTAGCAAATTACC‑C‑CCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGcac                                     <  2:625471/114‑1 (MQ=255)
                                                                                                                        cTCGGGTAGCAAATTACC‑C‑CCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTACTTTATTGGTAGTAAca            <  2:606917/139‑1 (MQ=255)
                                                                                                                        cTCGGGTAGCAAATTACC‑C‑CCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTACTTTATTGGTAGTAAca            >  1:97113/1‑139 (MQ=255)
                                                                                                                         tCGGGTAGCAAATTACC‑C‑CCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTtata                                                                    <  1:1062871/82‑1 (MQ=255)
                                                                                                                         tCGGGTAGCAAATTACC‑C‑CCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTtata                                                                    >  2:1062871/1‑82 (MQ=255)
                                                                                                                             gTAGCAAATTACC‑C‑CCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGAt                               <  1:815086/115‑1 (MQ=255)
                                                                                                                             gTAGCAAATTACC‑C‑CCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGAt                               >  2:815086/1‑115 (MQ=255)
                                                                                                                               aGCAAATTACC‑C‑CCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTACTTTATTGGTAGTAACATCATTAc     <  2:256881/139‑1 (MQ=255)
                                                                                                                                 cAAATTACC‑C‑CCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTACTTTATTGGTAGTAACATCATTACca   >  1:340930/1‑139 (MQ=255)
                                                                                                                                  aaaTTACC‑C‑CCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTACTTTATTGGTAGTAACATCATTACcag  <  2:340930/139‑1 (MQ=255)
                                                                                                                                        |                                                                                                                                      
CGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑C‑C‑CCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTACTTTATTGGTAGTAACATCATTACCAG  >  NC_000913/2484756‑2485023

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ 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