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 F71 I1 R1 21 57.4 2535598 87.8% 2226255 142.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 481,846 G→A T853I (ACC→ATC)  acrB ← multidrug efflux pump RND permease AcrB

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913481,8460GA95.8% 106.7 / NA 50T853I (ACC→ATC) acrBmultidrug efflux pump RND permease AcrB
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (21/25);  minor base C (2/0);  total (23/27)
Fisher's exact test for biased strand distribution p-value = 2.24e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGAACGGAATCGACCAGCTCTCGTACAGCGCCGCCAGACACAGGAACACGACAATCAACGAAATCGCGTACAGTGAAGGTGCCTGGTTGCCGGAGAGACGTTCCTGATAGGACATCCCCGTCCAGTCATAGCCAACACCGGTAGGCAGTTTGCTCGCCAGTTGTTCCATCAGCTCCATTGCTTCACCGGTACTTTTACCCGGTGCCGCCTGGCCTAAGATTTCCATGGATGGCAGGCCGTTGTAACGTTCCAGACGCGGCGAACCGTACTCCCAACGAGA  >  NC_000913/481706‑481985
                                                                                                                                            |                                                                                                                                           
agaACGGAATCGACCAGCTCTCGTACAGCGCCGCCAGACACAGGAACACGACTATCATCTTATTCGCGTACAGTGAAGGTGCCTGGTTGCCGGAGAGACGTTCCTGATAGGACATCCCCGTCCAGTCATAGCCAACACCGATa                                                                                                                                           <  1:716068/143‑1 (MQ=255)
    cGGAATCGACCAGCTCTCGTACAGCGCCGCCAGACACAGGAACACTTCTATCTTCGTAATCGCGTACAGTGAAGGTGCCTGGTTGCCGGAGAGACGTTCCTGATAGGACATCCCCGTCCAGTCATAGCCAACACCGATAGGCa                                                                                                                                       <  1:669056/143‑1 (MQ=255)
       gaTCGACCAGCTCTCGTACAGCGCCGCCAGACACAGGAGCACGACAATCAACGAAATCGCGTACAGTGAAGGTGCCTGGTTGCCGGAGAGACGTTCCTGATAGGACATCCCCGTCCAGTCATAGCCAACACCGATAGGCAGtt                                                                                                                                    <  2:1143241/142‑1 (MQ=255)
       aaTCGACCAGCTCTCGTACAGCGCCGCCAGACACAGGAACACGACAATCAACGAAATCGCGTACAGTGAAGGTGCCTGGTTGCCGGAGAGACGTTCCTGATAGGACATCCCCGTCCAGTCATAGCCAACACCGCTAGGCAGtt                                                                                                                                    >  2:326281/1‑143 (MQ=255)
         tCGACCAGCTCTCGTACAGCGCCGCCAGACACAGGAACACGACAATCAACGAAATCGCGTACAGTGAAGGTGCCTGGTTGCCAGAGAGACGATCCTGATAAGAAATCCCCGACCAGTCATAACAAACACAGATAGGCAGTTTg                                                                                                                                  >  1:490763/1‑143 (MQ=255)
            aCCAGCTCTCGTACAGCGCAGCCAGACACAGGAACACGACAATCAACGAAATCGCGTACAGTGAAGGAACCTGGTTGCCGGATAGACGTTCGTGATAGGACATACCCGTCCAGTAGTAGCCAACACCGCTAGGCAGTTTGCTc                                                                                                                               >  2:1165078/1‑143 (MQ=255)
                gCTCTCGTACAGCGCCGCCAGACACAGGAACACGTCAATCTTCGTAATTGTGTACAGTGAAGGTGCCTGGTTGCCGGAGAGACGTTCCTGATAGGACATCCCCGTCCAGTCATAGCCAACACCGATAGGCAGTTTGCTCGCCa                                                                                                                           <  1:47462/143‑1 (MQ=255)
                 ttcacGTACAGATCCGCTATATACATGATTACGACAATCAACGAAAACGCCGACAGGGAAGGTGCCTGGTTGCCGGAGAGACGTTCCTGATAGGACATCCCCGTCCAGTCATAGCCAACACCGATAGGCAGTTTGCTCGCCAg                                                                                                                          <  1:218232/139‑1 (MQ=255)
                        aCAGCGCCGCCAGACACAGGAACACGACAATCAACGAAATCGCGTACAGTGGAGGTGCCTGGTTGCCGGAGAGACGTTCCTGATAGGACATCCCCGTCCAGTCATAGCCAACACCTATACGCAGATTGCTAGCCAgttgttac                                                                                                                   >  1:682676/1‑141 (MQ=255)
                          aGCGCCGCCAGACACAGGAACACGACAATCAACGAAATCGCGTACAGTGAAGGTGCCTGGTTGCCGGAGAGACGTTCCTGATAGGACATCCCCGTCCAGTCATAGCCAACACCGATAGACAGTTTGCTCGCCAATTGTTCAAt                                                                                                                 >  1:1035939/1‑143 (MQ=255)
                                                   cAATCAACGAACTCGCGTACAGTGAAGGTGCCTGGTTGCCGTAGAGACTTTCCTGATAGTACATCCCCGTCCAGTCATAGCCAACACCGATAGGCAGTTTGCTCGCCAGTTGTTCCATCAGCTCCATTGCTTCACCGGTACtt                                                                                        <  1:155432/143‑1 (MQ=255)
                                                      tCAACGAAATCGCGTACAGTGAAGGTGCCTGGTTGCCGGAGAGACGTTCCTGATAGGACATCCCCGTCCAGTCATCGCCACCACCCATAGGCCGTTTGCTCGCCAGTTGTTCCATAAGCTCCATTTCTTAACCGGTACTTTTa                                                                                     >  1:61639/1‑143 (MQ=255)
                                                       cgaCGAAATCGCGTACAGTGAAGGTGCCTGGTTGCCGGAGAGACGTTCCTGATAGGACATCCCCGTCCAGTCATAGCCAACACCGATATGCAGTTTGCTCTCCAGTTGTTCCATCAGCTCCATTGCTTCACCGGTACTTTTAc                                                                                    <  2:565085/141‑1 (MQ=255)
                                                                    tACAGTGAAGGTGCCTGGTTGCCGGAGAGACGTTCCTGATAGGACATCCCCGTCCAGTCATAGCCAACACCGATAGGCAGTTTGCTCGCCAGTTGTTCCATCAGCTCCATTGCTTCACCGGTACTTTTACCCGGTGCCGCCTg                                                                       <  1:983801/143‑1 (MQ=255)
                                                                    gagaGTGAAGGTGCGTGTTTGTAGTAGAGACGTGCCTGATAGGACATCCCCGTCCAGTCATAGCCTACACCGATAGGCAGTGTGCTCGCCAGTGGTTCCATCAGCTCCATTGCTTCACCGGTACTTTTACCCGGTGCCGCCTg                                                                       <  2:947519/140‑1 (MQ=255)
                                                                           aaGGTGCCTGGTTGCCGGAGAAACGTTACTGATAGGACATCCCCGTCCAGTCATAGCCAACACCGACAGGCCGTTTGCTCCCCAGTTGTTCAATCAGCCCCATTGCTTCACCGGTACTCTTACCCGGTGCCGCCTGGCCTagg                                                                >  2:320707/1‑141 (MQ=255)
                                                                             ggTGCCTGGTGGCGGGAGAGACGTGTCTGGTAGGACATCCCGGTCCAGTCATAGCCAACACCGATAGGCAGTTTGCTCGCCAGTTGTTCCATCGTCTCCATTGCTTCACCGGTACTTTTACCCGGTGCCGCCTGGCCTAAGAt                                                              <  2:285615/143‑1 (MQ=255)
                                                                              gTGCCTGGTTGCCGGAGAGACGTTCCTGATAGGACATCCCCGTCCAGTCATAGCCAACACCGATAGGCAGTTTGCTCGCCAGTTGTTCCATCAGCTCCATTGCTTCACCGGTACTTTTACCCGCTGCCGCCTGGCCTAATAtt                                                             >  1:167313/1‑143 (MQ=255)
                                                                               tGCCTGGTTGCCGGAGAGACGTTCCTGATAGGACATCCCCGTCCAGTCATAGCCAACACCGATAGGCAGTTTGCTCGCCAGTTGTTCCATCAGCTCCATTGCTAAACCGGTACTTTTACACGGTGCAGACTGGCCTAGGAttt                                                            >  1:179745/1‑143 (MQ=255)
                                                                                gCCTGGTTGCCGGAGAGACGTTCCTGATAGGACATCCCCGTCCAGTCATAGCCAACACCGATAGGCAGTTTGCTCGCCAGTTGTTCCATCAGCACCATCGCTTCACCGGTACGTTTACCCGGTGCCGCCTGGCCGAAGCTTTc                                                           >  2:1182408/1‑143 (MQ=255)
                                                                                 ccTGGTTGCCGGAGAGACGTTCCTGATAGGACATCCCCGTCCAGTCATAGCCAACACCGATAGGCAGTTTGCTCGCCAGTTGTTCCATCAGCTCCATTGCTTCACCGGTACTTTTACCCGGTGCCGCCTGGCCTAAGATTTcc                                                          <  2:302052/143‑1 (MQ=255)
                                                                                  cTGGTTGCCGGAGAGACGTTCCTGATAGGACATCCCCGTCCAGTCATAGCCAACACCGATAGGCAGTTAGCCCGCCAGTTGTTCCATCAGCTCCATTGCTTCACCGGTACTTTTACCCGGTGCCGCCTGGCCTAAGATTTCCa                                                         <  1:326281/143‑1 (MQ=255)
                                                                                     gTTGCCGGAGAGACGTTCCTGATAGGACATCCCCGTCCAGTCATAGCCAACACCGATAGGCAGTTTGCTCGCCGGTTGTTCCATCAGCTCCATTGCTTCACCGGTACTTTTACCCGGTGCCGCCTGGCCTAAGATTTCCatgg                                                      <  2:1251180/143‑1 (MQ=255)
                                                                                      ttGCCGGAGAGACGTTCCTGATAGGACAGCCCCGTCCAGTCATAGCCAACACCGATAGGCAGTTTGCTCGCCAGTTGTTCCATCAGCTCCATTGCTTCACCGGTACTTTTACCCGGTGCCGCCTGGCCTAAGATTTCCatgga                                                     <  2:108795/143‑1 (MQ=255)
                                                                                         ccGGAGAGACGTTCCTGATAGGACCTCCCCGTCCAGTCATAGCCAACACCGATAGGCAGTTTGCTCGCCAGTTGTTAAATAAACTCCATTACTTCAACGGTACTTTTACCCGGTCCCGCCTGGCCTAAGATTTCCatggatgg                                                  >  1:458749/1‑143 (MQ=255)
                                                                                         ccGGAGAGACGTTCCTGATAGGACATCCCAGTCCAGTCATAGCCAACACCGATCGGCAGTTTGCTCGCCAGTTGTTCCATCAGCTCCATTGCTTCACCGGTACTTTTACCCGGTGCCGCCTGGCCTAAGATTTCCatggatgg                                                  >  2:66305/1‑143 (MQ=255)
                                                                                          cGGAGAGACGTTCCTGATAGGACATCCCCGTCCAGTCATAGCCAACACCGATAGGCAGTTTGCTCGCCAGTTGTTCCATCAGCTCCATTGCTTCACCGGTACTTTTACCCGGTGCCGCCTGGCCTAAGATTTCCATGGATGGc                                                 >  1:894974/1‑143 (MQ=255)
                                                                                          cGGAGAGACGTTCCTGATAGGACATCCCCGTCCAGTCATAGCCAACACCGATAGGCAGTTTGCTCGCCAGTTGTTCCATCAGCTCCATTGCTTCACCGGTACTTTTACCCGGTGCCGCCTGGCCTAAGATTTCCATGGATGGc                                                 >  2:227340/1‑143 (MQ=255)
                                                                                           gcagagaCTTTCCTGATAGTACATCCCCGTCCAGTCATCGCCAACACCGATATTCATTTTGCTCGCCAGTTGTTCCATCAGCTCCATTGCTGCACCGGTACTTTTACCCGGTGCCGCCTGGCCTAAGATTTCCATGGATGGCa                                                <  1:542350/141‑1 (MQ=255)
                                                                                               agaCGTTCCTGATAGGACATCCCCGTCCAGTCATAGCCAACACCGATAGGCAGTTTGCTCGCCAGTTGTTCCATCAGCTCCATTGCTTCACCGGTACTTTTACCCGGTGCCGCCTGGCCTAAGATTTCCATGGATGGCAGGcc                                            <  2:1181879/143‑1 (MQ=255)
                                                                                                  cGTTCCTGATGGGACATCCAAGATCAGTCAGAGCCAACACCGATAGGCAGTTTGCTCGCCAGTTGTTCCATCAGCTCCATTGCTTCACCGGTACTTTTACCCGGTGCCGCCTGGCCTAAGATTTCCATGGATGGCAGGCCGtt                                         <  2:929484/143‑1 (MQ=255)
                                                                                                  cGTTCCTGATAGGACATCCCCGTCCAGTCATAGCCAACACCGATAGGCAGTTTGCTCGCCAGTTGTTCCATCAGCTCCATTGCTTCACCGGTACTTTTACCCGGTGCCGCCTGGCCTAAGATTTCCATGGATGGCAGGCCGtt                                         <  2:894974/143‑1 (MQ=255)
                                                                                                   gTTCCTGATAGGACCTCCCCGTCCAGTCATAGCCAACACCGATAGGCAGTTTGCTCGCCAGTTGTTCCATCAGCTCCATTGCTTCACCGGTACTTTTACCCGGTGCCGCCTGGCCTAAGATTTCCATGGATGGCAGGCCGTTg                                        <  2:577856/143‑1 (MQ=255)
                                                                                                      ccTGATAGGACATCCCCGTCCAGTCATAGCCAACACCGATAGGCAGTTTGCTCGCCAGTTGTTCCCTCAGCTCCATTTCTTCACCGGTACTTTTCCCAGGTGCCGCCTGGCCAAAGATTTCAATGGATAGCAGGCAGtcgaaa                                     >  1:1203269/1‑138 (MQ=255)
                                                                                                      ccTGATAGGACATCCCCGTCCAGTCATAGCCAACACCGATAGGCAGTTTGCTCGCCAGTTGTTCCATCAGCTCCATTGCTTCACCGGTACTTTTACCCGGTGCCGCCTGGCCTAAGATTTCCATGGATGGCAGGCCGTTGTaa                                     <  1:227340/143‑1 (MQ=255)
                                                                                                          aTAGGACATCCCCGTCCAGTCATAGCCAACATCGATAGGTAGTTTTCTCGCCAGTTGTTCCATCAGCTCCATTGCTTCACCGGTACTTTTACCCGGTGCCGCCTGGCCTAAGAGTTCCATGGATGGCAGGCCGTTGTAACGtt                                 <  1:491253/143‑1 (MQ=255)
                                                                                                             cgACATCCCCGTCCAGTCATAGCCAACACCGATAGGCAGTTTGCTCGCCAGTTGTTCCATCAGCTCCATTGCTTCACCGGTACTTTTACCCGGTGCCGCCTGGCCTAAGATTTCCATGGATGGCAGGCCGTTGTAACGTTCCa                              <  1:713138/142‑1 (MQ=255)
                                                                                                                cATCCCCGTCCAGTCATAGCCAACACCGATAGGCAGTTTGCTCGCCAGTTGTTCCATCAGCTCCATTGCTTCACCGGTACTTTTACCCGGTGCCGCCTCGCCTAAGATTTCCGTGGATGGCTGGCCGTCGCAACGtcacagcc                           >  2:402459/1‑136 (MQ=255)
                                                                                                                  tCCCCGTCCAGTCATAGCCAACACCGATAGGCAGTTTGCTCGCCAGTTGTTCCATCAGCTCCATTGCTTCACCGGTACTTTTACCCGGTGCCGCCTGGCCTAACATTTCCATGGATGGCAGGCCGTTGTAACGTTCCAGAcgc                         >  1:98254/1‑143 (MQ=255)
                                                                                                                     cctttcAGTCATATCCAATTTCGATAGTCAGTTTGCTGCCCAGTTGTTTCATCAGTTCCATTGCTTCACCGGGACTGTTACCCGGTGCCGCCGGGCCTAAGATTTCCATGGATGGCAGGCCGTTGTAACGTTCCAGACgcggc                      <  1:96502/138‑1 (MQ=255)
                                                                                                                     ccGTCCAGTCATAGCCAACACCGTTAGGCTGTTTGCTTTCCAGTTGTTCTATCAGCTCCATTGCTTCACCGGTACGTTTACCCGGTGCCGCCTGGCCTAAGATTTCCATGGATGGCAGGCCGTTGTAACGTTCCAGACgcggc                      <  1:523560/143‑1 (MQ=255)
                                                                                                                     ccGTCCAGTCATAGCCAACACCGATAGGCAGTCTGCTCGCCAGTTGTTCCATCAGCTCCATTGCTTCACCGGGAATTTTACCCGGTGCCGCCTGCCCTACGATTTCCATGGACGGCAGGCCGTCGCAACGTACCAGaacgagc                      >  2:408146/1‑137 (MQ=255)
                                                                                                                          cAGTCATAGCCAACACCGTTAGGCAGTTTGCTCGCCTGTTGTTCCATCAGCTCCATTGCTGCACCGGTACTTTTACCCGGTGCCGCCTGGCCTAAGATTTCCATGGATGGCAGGCCGTTGTAACGTTCCAGACGCGGCGAAcc                 <  1:1165078/143‑1 (MQ=255)
                                                                                                                           aGTCATAGCCAACACCGATAGGCAGTTTGCTCGCCAGTTGTTCCATCAGCTCAATTGCTTCAGCGGTACTTTTACTCGGTGCCCCCTGGCCTAAGATACCCACTGATGACAGGCCGTGGTGACGATCCACACGCGGCGCACCg                >  2:394085/1‑143 (MQ=255)
                                                                                                                           aGTCATAGCCAACACCGATAGACAGTTTGCTCGCCAGTTGTTCCATCAGCTCCATTGCTTCACCGGTACTTTTACCCGGTGCCGCCTGGCCTAAGATTTCCATGCATGGCAGGCCGTTGTAACGTTCCAGACGCGGCGAACCg                >  2:676630/1‑143 (MQ=255)
                                                                                                                                    cAACACCGATAGGCAGTTTGCTCGCCAGTTGTTCCATCAGCTCCATTGCTTCACCGGTACTTTTTCCCTGTGCCGCCTGGCCTAAGATTCCCATGGATGGCAGGCCGTTGTAACGTTCCAGACGCGGCGAACCGTACTCCCaa       <  1:793238/143‑1 (MQ=255)
                                                                                                                                     aaCACCGATAGGCAGTTTGCTCGCCAGTTGTTCCATCAGCTCCATTGCTTCACCGGTACTTTTACCCGGTGCCGCCTGGCCTAAGATTTCCATGGATGGCAGGCCGTTGTAACGTTCCCGCCGCGGCGAACCGTACTCCCAAc      >  1:690740/1‑143 (MQ=255)
                                                                                                                                     aaCACCGATAGGCAGTTTGCTCGCCAGTTGTTCCATCAGCTCCATTGCTTCACCGGTACTTTTACCCGGTGCCGCCTGGCCTAAGATTTCCATGGATGGCAGGCCGTTGTAACGTTCCAGACGCGGCGCACCGTACTCCCAAc      >  1:849536/1‑143 (MQ=255)
                                                                                                                                        acCGATAGGCAGTTTGCTCGCCAGTTGTTCCATCAGCTCCATTGCTTCACCGGTACTTTTACCCGGTGCCGCCTGGCCTAAGATTTCCATGGATGGCAGGCCGTTGTAACGTTCCAGACGAGGCGAACCGTACTCCCCACgac   >  2:53262/1‑142 (MQ=255)
                                                                                                                                         ccGATAGGCAGTTTGCTCGCCAGTTGTTCCATCAGCTCCATTGCTTCACCGGTACTTTTACCCGGTGCCGCCTGGCCTAAGATTTCCATGGATGGCAGGCCGTTGTAACGTTCCAGACGCGGCGAACCGTACTCCCAACgaga  <  1:66305/143‑1 (MQ=255)
                                                                                                                                            |                                                                                                                                           
AGAACGGAATCGACCAGCTCTCGTACAGCGCCGCCAGACACAGGAACACGACAATCAACGAAATCGCGTACAGTGAAGGTGCCTGGTTGCCGGAGAGACGTTCCTGATAGGACATCCCCGTCCAGTCATAGCCAACACCGGTAGGCAGTTTGCTCGCCAGTTGTTCCATCAGCTCCATTGCTTCACCGGTACTTTTACCCGGTGCCGCCTGGCCTAAGATTTCCATGGATGGCAGGCCGTTGTAACGTTCCAGACGCGGCGAACCGTACTCCCAACGAGA  >  NC_000913/481706‑481985

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A