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
A4 F28 I1 R1 159 82.1 2830106 99.3% 2810295 139.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,297,114 (C)7→8 coding (531/624 nt) ccmA ← heme trafficking system ATP‑binding protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,297,1071.C95.5% 153.3 / 0.0 44coding (538/624 nt)ccmAheme trafficking system ATP‑binding protein
Reads supporting (aligned to +/- strand):  ref base . (0/2);  new base C (19/23);  total (19/25)
Fisher's exact test for biased strand distribution p-value = 4.98e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.81e-01

CGCTATGGCGAAACGCTACACGCAGCTCAAGACGGAAAATGCGCCAGAACATCATGCGGCCCTCGTTTGCGTCAGTGAAATGCGGCGAATTTTACTTTCAGCAACGTTGAGCGGCTGGTGGGTAGTCAGAATCACAAT‑‑CCCCCCCTGCTCCGTATGCTGCGCCATACGCTGGGTCAGACGATCGACACCGTTAACGTCAATCGCGGTAAAAGGCTCGTCGAGGATCCATAACGTGGCACGGGTCAGCCACAGACGCGCTAAAGCGACGCG  >  NC_000913/2296970‑2297239
                                                                                                                                          |                                                                                                                                     
cgcTATGGCGAAACGCTACACGCAGCTCAAGACGGAAAATGCGCCAGAACATCATGCGGCCCTCGTTTGCGTCAGTGAAATGCGGCGAATTTTACTTTCAGCAACGTTGAGCGGCTGGTGGGTAGTCAGAATCACAAT‑‑cc                                                                                                                                    <  2:1395541/140‑1 (MQ=255)
     tGGCGAAACGCTACACGCAGCTCAAGACGGAAAATGCGCCAGAACATCATGCGGCCCTCGTTTGCGTCAGTGAAATGCGGCGAATTTTACTTTCAGCAACGTTGAGCGGCTGGTGGGTAGTCAGAATCACAAT‑‑ccccccc                                                                                                                               <  1:1085485/140‑1 (MQ=255)
     tGGCGAAACGCTACACGCAGCTCAAGACGGAAAATGCGCCAGAACATCATGCGGCCCTCGTTTGCGTCAGTGAAATGCGGCGAATTTTACTTTCAGCAACGTTGAGCGGCTGGTGGGTAGTCAGAATCACAAT‑‑ccccccc                                                                                                                               <  1:904992/140‑1 (MQ=255)
     tGGCGAAACGCTACACGCAGCTCAAGACGGAAAATGCGCCAGAACATCATGCGGCCCTCGTTTGCGTCAGTGAAATGCGGCGAATTTTACTTTCAGCAACGTTGAGCGGCTGGTGGGTAGTCAGAATCACAAT‑‑ccccccc                                                                                                                               <  2:193215/140‑1 (MQ=255)
     tGGCGAAACGCTACACGCAGCTCAAGACGGAAAATGCGCCAGAACATCATGCGGCCCTCGTTTGCGTCAGTGAAATGCGGCGAATTTTACTTTCAGCAACGTTGAGCGGCTGGTGGGTAGTCAGAATCACAAT‑‑ccccccc                                                                                                                               <  2:365260/140‑1 (MQ=255)
       gCGAAACGCTACACGCAGCTCAAGACGGAAAATGCGCCAGAACATCATGCGGCCCTCGTTTGCGTCAGTGAAATGCGGCGAATTTTACTTTCAGCAACGTTGAGCGGCTGGTGGGTAGTCAGAATCACAAT‑‑cccccccct                                                                                                                             <  1:415756/140‑3 (MQ=255)
          aaaCGCTACACGCAGCTCAAGACGGAAAATGCGCCAGAACATCATGCGGCCCTCGTTTGCGTCAGTGAAATGCGGCGAATTTTACTTTCAGCAACGTTGAGCGGCTGGTGGGTAGTCAGAATCACAAT‑‑cccccccctgct                                                                                                                          >  1:945474/1‑135 (MQ=255)
          aaaCGCTACACGCAGCTCAAGACGGAAAATGCGCCAGAACATCATGCGGCCCTCGTTTGCGTCAGTGAAATGCGGCGAATTTTACTTTCAGCAACGTTGAGCGGCTGGTGGGTAGTCAGAATCACAAT‑‑cccccccctgct                                                                                                                          <  2:375557/140‑6 (MQ=255)
                   acGCAGCTCAAGACGGAAAATGCGCCAGAACATCATGCGGCCCTCGTTTGCGTCAGTGAAATGCGGCGAATTTTACTTTCAGCAACGTTGAGCGGCTGGTGGGTAGTCAGAATCACAAT‑‑CCCCCCCTGCTCCGTAtgctg                                                                                                                 <  1:417438/140‑1 (MQ=255)
                       aGCTCAAGACGGAAAATGCGCCAGAACATCATGCGGCCCTCGTTTGCGTCAGTGAAATGCGGCGAATTTTACTTTCAGCAACGTTGAGCGGCTGGTGGGTAGTCAGAATCACAATC‑CCCCCCCTGCTCCGTAtg                                                                                                                    >  1:1281458/1‑134 (MQ=255)
                       aGCTCAAGACGGAAAATGCGCCAGAACATCATGCGGCCCTCGTTTGCGTCAGTGAAATGCGGCGAATTTTACTTTCAGCAACGTTGAGCGGCTGGTGGGTAGTCAGAATCACAATC‑CCCCCCCTGCTCCGTAtg                                                                                                                    <  2:1281458/134‑1 (MQ=255)
                       aGCTCAAGACGGAAAATGCGCCAGAACATCATGCGGCCCTCGTTTGCGTCAGTGAAATGCGGCGAATTTTACTTTCAGCAACGTTGAGCGGCTGGTGGGTAGTCAGAATCACAATC‑CCCCCCCTGCTCCGTATGCTgcgc                                                                                                              >  2:1368441/1‑140 (MQ=255)
                       aGCTCAAGACGGAAAATGCGCCAGAACATCATGCGGCCCTCGTTTGCGTCAGTGAAATGCGGCGAATTTTACTTTCAGCAACGTTGAGCGGCTGGTGGGTAGTCAGAATCACAATC‑CCCCCCCTGCTCCGTATGCTgcgc                                                                                                              >  1:746878/1‑140 (MQ=255)
                        gCTCAAGACGGAAAATGCGCCAGAACATCATGCGGCCCTCGTTTGCGTCAGTGAAATGCGGCGAATTTTACTTTCAGCAACGTTGAGCGGCTGGTGGGTAGTCAGAATCACAATC‑CCCCCCCTGCTCCGTATGCTGCGcc                                                                                                             >  2:258018/1‑140 (MQ=255)
                        gCTCAAGACGGAAAATGCGCCAGAACATCATGCGGCCCTCGTTTGCGTCAGTGAAATGCGGCGAATTTTACTTTCAGCAACGTTGAGCGGCTGGTGGGTAGTCAGAATCACAATC‑CCCCCCCTGCTCCGTATGCTGCGcc                                                                                                             <  2:1224751/140‑1 (MQ=255)
                             aGACGGAAAATGCGCCAGAACATCATGCGGCCCTCGTTTGCGTCAGTGAAATGCGGCGAATTTTACTTTCAGCAACGTTGAGCGGCTGGTGGGTAGTCAGAATCACAAT‑‑CCCCCCCTGCTCCGTATGCTGCGCCATACGc                                                                                                       <  2:610425/140‑1 (MQ=255)
                               aCGGAAAATGCGCCAGAACATCATGCGGCCCTCGTTTGCGTCAGTGAAATGCGGCGAATTTTACTTTCAGCAACGTTGAGCGGCTGGTGGGTAGTCAGAATCACAATC‑CCCCCCCTGCTCCGTATGCTGCGCCATACGCt                                                                                                      >  2:4917/1‑140 (MQ=255)
                                 ggAAAATGCGCCAGAACATCATGCGGCCCTCGTTTGCGTCAGTGAAATGCGGCGAATTTTACTTTCAGCAACGTTGAGCGGCTGGTGGGTAGTCAGAATCACAATC‑CCCCCCCTGCTCCGTATGCTGCGCCATACGCTgg                                                                                                    >  2:445794/1‑140 (MQ=255)
                                   aaaaTGCGCCAGAACATCATGCGGCCCTCGTTTGCGTCAGTGAAATGCGGCGAATTTTACTTTCAGCAACGTTGAGCGGCTGGTGGGTAGTCAGAATCACAATC‑CCCCCCCTGCTCCGTATGCTGCGCCATACGCTGGGt                                                                                                  >  2:1197158/1‑140 (MQ=255)
                                   aaaaTGCGCCAGAACATCATGCGGCCCTCGTTTGCGTCAGTGAAATGCGGCGAATTTTACTTTCAGCAACGTTGAGCGGCTGGTGGGTAGTCAGAATCACAATC‑CCCCCCCTGCTCCGTATGCTGCGCCATACGCTGGGt                                                                                                  >  1:1063077/1‑140 (MQ=255)
                                    aaaTGCGCCAGAACATCATGCGGCCCTCGTTTGCGTCAGTGAAATGCGGCGAATTTTACTTTCAGCAACGTTGAGCGGCTGGTGGGTAGTCAGAATCACAATC‑CCCCCCCTGCTCCGTATGCTGCGCCATACGCTGGGTc                                                                                                 <  2:50615/140‑1 (MQ=255)
                                      aTGCGCCAGAACATCATGCGGCCCTCGTTTGCGTCAGTGAAATGCGGCGAATTTTACTTTCAGCAACGTTGAGCGGCTGGTGGGTAGTCAGAATCACAATC‑CCCCCCCTGCTCCGTATGCTGCGCCATACGCTGGGTCAg                                                                                               <  2:592357/140‑1 (MQ=255)
                                      aTGCGCCAGAACATCATGCGGCCCTCGTTTGCGTCAGTGAAATGCGGCGAATTTTACTTTCAGCAACGTTGAGCGGCTGGTGGGTAGTCAGAATCACAATC‑CCCCCCCTGCTCCGTATGCTGCGCCATACGCTGGGTCAg                                                                                               <  1:609812/140‑1 (MQ=255)
                                        gcgcCAGAACATCATGCGGCCCTCGTTTGCGTCAGTGAAATGCGGCGAATTTTACTTTCAGCAACGTTGAGCGGCTGGTGGGTAGTCAGAATCACAATC‑CCCCCCCTGCTCCGTATGCTGCGCCATACGCTGGGTCAGAc                                                                                             <  2:1063077/140‑1 (MQ=255)
                                           ccAGAACATCATGCGGCCCTCGTTTGCGTCAGTGAAATGCGGCGAATTTTACTTTCAGCAACGTTGAGCGGCTGGTGGGTAGTCAGAATCACAATC‑CCCCCCCTGCTCCGTATGCTGCGCCATACGCTGGGTCAGACGAt                                                                                          <  1:799453/140‑1 (MQ=255)
                                              gAACATCATGCGGCCCTCGTTTGCGTCAGTGAAATGCGGCGAATTTTACTTTCAGCAACGTTGAGCGGCTGGTGGGTAGTCAGAATCACAATC‑CCCCCCCTGCTCCGTATGCTGCGCCATACGCTGGGTCAGACGATCGa                                                                                       <  1:68791/140‑1 (MQ=255)
                                                      tGCGGCCCTCGTTTGCGTCAGTGAAATGCGGCGAATTTTACTTTCAGCAACGTTGAGCGGCTGGTGGGTAGTCAGAATCACAATC‑CCCCCCCTGCTCCGTATGCTGCGCCATACGCTGGGTCAGACGATCGACACCGTTa                                                                               >  1:445050/1‑140 (MQ=255)
                                                      tGCGGCCCTCGTTTGCGTCAGTGAAATGCGGCGAATTTTACTTTCAGCAACGTTGAGCGGCTGGTGGGTAGTCAGAATCACAATC‑CCCCCCCTGCTCCGTATGCTGCGCCATACGCTGGGTCAGACGATCGACACCGTTa                                                                               >  1:1229185/1‑140 (MQ=255)
                                                           cccTCGTTTGCGTCAGTGAAATGCGGCGAATTTTACTTTCAGCAACGTTGAGCGGCTGGTGGGTAGTCAGAATCACAATC‑CCCCCCCTGCTCCGTATGCTGCGCCATACGCTGGGTCAGACGATCGACACCGTTAACGTc                                                                          >  1:620605/1‑140 (MQ=255)
                                                            ccTCGTTTGCGTCAGTGAAATGCGGCGAATTTTACTTTCAGCAACGTTGAGCGGCTGGTGGGTAGTCAGAATCACAATC‑CCCCCCCTGCTCCGTATGCTGCGCCATACGCTGGGTCAGACGATCGACACCGTTAACGTCa                                                                         >  2:769796/1‑140 (MQ=255)
                                                              tCGTTTGCGTCAGTGAAATGCGGCGAATTTTACTTTCAGCAACGTTGAGCGGCTGGTGGGTAGTCAGAATCACAATC‑CCCCCCCTGCTCCGTATGCTGCGCCATACGCTGGGTCAGACGATCGACACCGTTAACGTCAAt                                                                       <  1:1197158/140‑1 (MQ=255)
                                                                      gTCAGTGAAATGCGGCGAATTTTACTTTCAGCAACGTTGAGCGGCTGGTGGGTAGTCAGAATCACAATC‑CCCCCCCTGCTCCGTATGCTGCGCCATACGCTGGGTCAGACGATCGACACCGTTAACGTCAATCGCGGTaa                                                               <  1:992709/140‑1 (MQ=255)
                                                                          gTGAAATGCGGCGAATTTTACTTTCAGCAACGTTGAGCGGCTGGTGGGTAGTCAGAATCACAATC‑CCCCCCCTGCTCCGTATGCTGCGCCATACGCTGGGTCAGACGATCGACACCGTTAACGTCAATCGCGGTAAAAgg                                                           <  1:1368441/140‑1 (MQ=255)
                                                                                 gcggcgAATTTTACTTTCAGCAACGTTGAGCGGCTGGTGGGTAGTCAGAATCACAATC‑CCCCCCCTGCTCCGTATGCTGCGCCATACGCTGGGTCAGACGATCGACACCGTTAACGTCAATCGCGGTAAAAGGCtcgtcg                                                    <  2:137824/140‑1 (MQ=255)
                                                                                 gcggcgAATTTTACTTTCAGCAACGTTGAGCGGCTGGTGGGTAGTCAGAATCACAATC‑CCCCCCCTGCTCCGTATGCTGCGCCATACGCTGGGTCAGACGATCGACACCGTTAACGTCAATCGCGGTAAAAGGCtcgtcg                                                    <  2:746878/140‑1 (MQ=255)
                                                                                    gcgAATTTTACTTTCAGCAACGTTGAGCGGCTGGTGGGTAGTCAGAATCACAATCCCCCCCCCTGCTCCGTATGCTGCGCCATACGCTGGGTCAGACGATCGACACCGTTAACGTCAATCGCGGTAAAAGGCTCGTCGAg                                                  <  2:1336471/140‑1 (MQ=255)
                                                                                    gcgAATTTTACTTTCAGCAACGTTGAGCGGCTGGTGGGTAGTCAGAATCACAATCCCCCCCCCTGCTCCGTATGCTGCGCCATACGCTGGGTCAGACGATCGACACCGTTAACGTCAATCGCGGTAAAAGGCTCGTCGAg                                                  >  1:1336471/1‑140 (MQ=255)
                                                                                         ttttACTTTCAGCAACGTTGAGCGGCTGGTGGGTAGTCAGAATCACAATC‑CCCCCCCTGCTCCGTATGCTGCGCCATACGCTGGGTCAGACGATCGACACCGTTAACGTCAATCGCGGTAAAAGGCTCGTCGAGGATCCa                                            <  2:1231765/140‑1 (MQ=255)
                                                                                         ttttACTTTCAGCAACGTTGAGCGGCTGGTGGGTAGTCAGAATCACAATC‑CCCCCCCTGCTCCGTATGCTGCGCCATACGCTGGGTCAGACGATCGACACCGTTAACGTCAATCGCGGTAAAAGGCTCGTCGAGGATCCa                                            <  1:1334766/140‑1 (MQ=255)
                                                                                            tACTTTCAGCAACGTTGAGCGGCTGGTGGGTAGTCAGAATCACAATC‑CCCCCCCTGCTCCGTATGCTGCGCCATACGCTGGGTCAGACGATCGACACCGTTAACGTCAATCGCGGTAAAAGGCTCGTCGAGGATCCATaa                                         <  1:769796/140‑1 (MQ=255)
                                                                                             aCTTTCAGCAACGTTGAGCGGCTGGTGGGTAGTCAGAATCACAATC‑CCCCCCCTGCTCCGTATGCTGCGCCATACGCTGGGTCAGACGATCGACACCGTTAACGTCAATCGCGGTAAAAGGCTCGTCGAGGATCCATAAc                                        <  1:445794/140‑1 (MQ=255)
                                                                                                  cAGCAACGTTGAGCGGCTGGTGGGTAGTCAGAATCACAATC‑CCCCCCCTGCTCCGTATGCTGCGCCATACGCTGGGTCAGACGATCGACACCGTTAACGTCAATCGCGGTAAAAGGCTCGTCGAGGATCCATAACGTGGc                                   <  1:4917/140‑1 (MQ=255)
                                                                                                   aGCAACGTTGAGCGGCTGGTGGGTAGTCAGAATCACAATC‑CCCCCCCTGCTCCGTATGCTGCGCCATACGCTGGTTCAGACGATCGACACCGTTAACGTCAATCGCGGTAAAAGGCTCGTCGAGGATCCATAACGTGGCa                                  <  2:1242041/140‑1 (MQ=255)
                                                                                                        cGTTGAGCGGCTGGTGGGTAGTCAGAATCACAATC‑CCCCCCCTGCTCCGTATGCTGCGCCATACGCTGGGTCAGACGATCGACACCGTTAACGTCAATCGCGGTAAAAGGCTCGTCGAGGATCCATAACGTGGCACGGGt                             <  2:945474/140‑1 (MQ=255)
                                                                                                          ttGAGCGGCTGGTGGGTAGTCAGAATCACAATC‑CCCCCCCTGCTCCGTATGCTGCGCCATACGCTGGGTCAGACGATCGACACCGTTAACATCAATCGCGGTAAAAGGCTCGTCGAGGATCCATAACGTGGCACGGGTCa                           >  2:479764/1‑140 (MQ=255)
                                                                                                                  cTGGTGGGTAGTCAGAATCACAATC‑CCCCCCCTGCTCCGTATGCTGCGCCATACGCTGGGTCAGACGATCGACACCGTTAACGTCAATCGCGGTAAAAGGCTCGTCGAGGATCCATAACGTGGCACGGGTCAGCCACAGa                   <  1:487704/140‑1 (MQ=255)
                                                                                                                    ggtggGTAGTCAGAATCACAATC‑CCCCCCCTGCTCCGTATGCTGCGCCATACGCTGGGTCAGACGATCGACACCGTTAACGTCAATCGCGGTAAAAGGCTCGTCGAGGATCCATAACGTGGCACGGGTCAGCCACAgtaa                 >  1:718361/1‑137 (MQ=255)
                                                                                                                    ggtggGTAGTCAGAATCACAATC‑CCCCCCCTGCTCCGTATGCTGCGCCATACGCTGGGTCAGACGATCGACACCGTTAACGTCAATCGCGGTAAAAGGCTCGTCGAGGATCCATAACGTGGCACGGGTCAGCCACAGAcg                 >  2:488560/1‑140 (MQ=255)
                                                                                                                           aGTCAGAATCACAATC‑CCCCCCCTGCTCCGTATGCTGCGCCATACGCTGGGTCAGACGATCGACACCGTTAACGTCAATCGCGGTAAAAGGCTCGTCGAGGATCCATAACGTGGCACGGGTCAGCCACAGACGCGCTaaa          >  2:192956/1‑140 (MQ=255)
                                                                                                                            gTCAGAATCACAATC‑CCCCCCCTGCTCCGTATGCTGCGCCATACGCTGGGTCAGACGATCGACACCGTTAACGTCAATCGCGGTAAAAGGCTCGTCGAGGATCCATAACGTGGCACGGGTCAGCCACAGACGCGCTAAAg         >  2:49813/1‑140 (MQ=255)
                                                                                                                               aGAATCACAATC‑CCCCCCCTGCTCCGTATGCTGCGCCATACGCTGGGTCAGACGATCGACACCGTTAACGTCAATCGCGGTAAAAGGTTCGTCGAGGATCCATAACGTGGCACGGGTCAGCCACAGACGCGCTAAAGCGa      >  2:97380/1‑140 (MQ=255)
                                                                                                                                   tCACAATC‑CCCCCCCTGCTCCGTATGCTACGCCATACGCTGGGTCAGACGATCGACACCGTTAACGTCAATCGCGGTAAAAGGCTCGTCGAGGATCCATAACGTGGCACGGGTCAGCCACAGACGCGCTAAAGCGAcgcg  <  1:3187/140‑1 (MQ=255)
                                                                                                                                          |                                                                                                                                     
CGCTATGGCGAAACGCTACACGCAGCTCAAGACGGAAAATGCGCCAGAACATCATGCGGCCCTCGTTTGCGTCAGTGAAATGCGGCGAATTTTACTTTCAGCAACGTTGAGCGGCTGGTGGGTAGTCAGAATCACAAT‑‑CCCCCCCTGCTCCGTATGCTGCGCCATACGCTGGGTCAGACGATCGACACCGTTAACGTCAATCGCGGTAAAAGGCTCGTCGAGGATCCATAACGTGGCACGGGTCAGCCACAGACGCGCTAAAGCGACGCG  >  NC_000913/2296970‑2297239

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