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
A14 F1 I1 R1 71 51.6 2219666 95.9% 2128659 118.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,650,996 C→T G431E (GGG→GAG)  yfhM ← bacterial alpha2‑macroglobulin colonization factor ECAM, anti‑host protease defense factor, periplasmic inner membrane‑anchored lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,650,9960CT98.3% 196.0 / NA 59G431E (GGG→GAG) yfhMbacterial alpha2‑macroglobulin colonization factor ECAM, anti‑host protease defense factor, periplasmic inner membrane‑anchored lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base T (29/29);  total (30/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATCCGATACTGATTATCGCCCGTGTTAGCGCGAATATGCCACATACCGGTTGCCGCATTGCTATCGAGTGGCCAGGTAAAGTGGTAGAGGCCATTCTCCGGCTGACTAACGACGCTCCTGAGTACCTGCCCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCATCACGCAGCAAACCATTGAGGATTACCGTTTCACCTGGGCGATAAAGATCGCGTGGGCCAAACATGAAAAACTGT  >  NC_000913/2650867‑2651130
                                                                                                                                 |                                                                                                                                      
aTCCGATACTGATTATCGCCCGTGTTAGCGCGAATATGCCACATACCGGTTGCCGCATTGCTATCGAGTGGCCAGGTAAAGTGGTAGAGGCCATTCTCCGGCTGACTAACGACGCTCCTGAGTACCTGCTCATCGGGtt                                                                                                                               <  2:827520/139‑1 (MQ=255)
 tCCGATACTGATTATCGCCCGTGTTAGCGCGAATATGCCACATACCGGTTGCCGCATTGCTATCGAGTGGCCAGGTAAAGTGGTAGAGGCCATTCTCCGGCTGACTAACGACGCTCCTGAGTACCTGCTCATCGGGttt                                                                                                                              >  2:107290/1‑139 (MQ=255)
    gATACTGATTATCGCCCGTGTTAGCGCGAATATGCCACATACCGGTTGCCGCATTGCTATCGAGTGGCCAGGTAAAGTGGTAGAGGCCATTCTCCGGCTGACTAACGACGCTCCTGAGTACCTGCTCATCGGGTTTAAt                                                                                                                           <  2:20446/139‑1 (MQ=255)
     aTACTGATTATCGCCCGTGTTAGCGCGAATATGCCACATACCGGTTGCCGCATTGCTATCGAGTGGCCAGGTAAAGTGGTAGAGGCCATTCTCCGGCTGACTAACGACGCTCCTGAGTACCTGCTCATCGGGTTTAATc                                                                                                                          >  2:72084/1‑139 (MQ=255)
     aTACTGATTATCGCCCGTGTTAGCGCGAATATGCCACATACCGGTTGCCGCATTGCTATCGAGTGGCCAGGTAAAGTGGTAGAGGCCATTCTCCGGCTGACTAACGAAGCTCCTGAGTACCTGCCCATCGGGTTTAATc                                                                                                                          >  1:89314/1‑139 (MQ=255)
           aTTATCGCCCGTGTTAGCGCGAATATGCCACATACCGGTTGCCGCATTGCTATCGAGTGGCCAGGTAAAGTGGTAGAGGCCATTCTCCGGCTGACTAACGACGCTCCTGAGTACCTGCTCATCGGGTTTAATCACGTCt                                                                                                                    >  1:426556/1‑139 (MQ=255)
           aTTATCGCCCGTGTTAGCGCGAATATGCCACATACCGGTTGCCGCATTGCTATCGAGTGGCCAGGTAAAGTGGTAGAGGCCATTCTCCGGCTGACTAACGACGCTCCTGAGTACCTGCTCATCGGGTTTAATCACGTCt                                                                                                                    >  2:554045/1‑139 (MQ=255)
           aTTATCGCCCGTGTTAGCGCGAATATGCCACATACCGGTTGCCGCATTGCTATCGAGTGGCCAGGTAAAGTGGTAGAGGCCATTCTCCGGCTGACTAACGACGCTCCTGAGTACCTGCTCATCGGGTTTAATCACGTCt                                                                                                                    >  1:131111/1‑139 (MQ=255)
              aTCGCCCGTGTTAGCGCGAATATGCCACATACCGGTTGCCGCATTGCTATCGAGTGGCCAGGTAAAGTGGTAGAGGCCATTCTCCGGCTGACTAACGACGCTCCTGAGTACCTGCTCATCGGGTTTAATCACGTCTAAc                                                                                                                 <  2:613673/139‑1 (MQ=255)
                  cccGTGTTAGCGCGAATATGCCACATACCGGTTGCCGCATTGCTATCGAGTGGCCAGGTAAAGTGGTAGAGGCCATTCTCCGGCTGACTAACGACGCTCCTGAGTACCTGCTCATCGGGTTTAATCACGTCt                                                                                                                    <  2:1093658/132‑1 (MQ=255)
                  cccGTGTTAGCGCGAATATGCCACATACCGGTTGCCGCATTGCTATCGAGTGGCCAGGTAAAGTGGTAGAGGCCATTCTCCGGCTGACTAACGACGCTCCTGAGTACCTGCTCATCGGGTTTAATCACGTCt                                                                                                                    >  1:1093658/1‑132 (MQ=255)
                      tgtTAGCGCGAATATGCCACATACCGGTTGCCGCATTGCTATCGAGTGGCCAGGTAAAGTGGTAGAGGCCATTCTCCGGCTGACTAACGACGCTCCTGAGTACCTGCTCATCGGGTTTAATCACGTCTa                                                                                                                   >  2:454303/1‑129 (MQ=255)
                      tgtTAGCGCGAATATGCCACATACCGGTTGCCGCATTGCTATCGAGTGGCCAGGTAAAGTGGTAGAGGCCATTCTCCGGCTGACTAACGACGCTCCTGAGTACCTGCTCATCGGGTTTAATCACGTCTa                                                                                                                   <  1:454303/129‑1 (MQ=255)
                      tgtTAGCGCGAATATGCCACATACCGGTTGCCGCATTGCTATCGAGTGGCCAGGTAAAGTGGTAGAGGCCATTCTCCGGCTGACTAACAACGCTCCTGAGTACCTGCTCATCGGGTTTAATCACGTCTAACTTGATggg                                                                                                         >  2:186274/1‑139 (MQ=255)
                          aGCGCGAATATGCCACATACCGGTTGCCGCATTGCTATCGAGTGGCCAGGTAAAGTGGTAGAGGCCATTCTCCGGCTGACTAACGACGCTCCTGAGTACCTGCTCATCGGGTTTAATCACGTCTAACTTGATGGGTTGa                                                                                                     <  2:304801/139‑1 (MQ=255)
                                 atatGCCACATACCGGTTGCCGCATTGCTATCGAGTGGCCAGGTAAAGTGGTAGAGGCCATTCTCCGGCTGACTAACGACGCTCCTGAGTACCTGCTCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCa                                                                                              >  1:984282/1‑139 (MQ=255)
                                        acaTACCGGTTGCCGCATTGCTATCGAGTGGCCAGGTAAAGTGGTAGAGGCCATTCTCCGGCTGACTAACGACGCTCCTGAGTACCTGCTCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCttt                                                                                       <  2:8878/139‑1 (MQ=255)
                                        acaGACCGGTTGCCGCATTGCTATCGAGTGGCCAGGTAAAGTGGTAGAGGCCATTCTCCGGCTGACTAACGACGCTCCTGAGTACCTGCTCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCttt                                                                                       <  1:945830/139‑1 (MQ=255)
                                           tACCGGTTGCCGCATTGCTATCGAGTGGCCAGGTAAAGTGGTAGAGGCCATTCTCCGGCTGACTAACGACGCTCCTGAGTACCTGCTCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTAcc                                                                                    <  1:934399/139‑1 (MQ=255)
                                              cGGTTGCCGCATTGCTATCGAGTGGCCAGGTAAAGTGGTAGAGGCCATTCTCCGGCTGACTAACGACGCTCCTGAGTACCTGCTCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTc                                                                                 >  2:105132/1‑139 (MQ=255)
                                                gTTGCCGCATTGCTATCGAGTGGCCAGGTAAAGTGGTAGAGGCCATTCTCCGGCTGACTAACGACGCTCCTGAGTACCTGCTCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTg                                                                               >  1:613298/1‑139 (MQ=255)
                                                 ttGCCGCATTGCTATCGAGTGGCCAGGTAAAGTGGTAGAGGCCATTCTCCGGCTGACTAACGACGCTCCTGAGTACCTGCTCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGc                                                                              >  1:46041/1‑139 (MQ=255)
                                                  tGCCGCATTGCTATCGAGTGGCCAGGTAAAGTGGTAGAGGCCATTCTCCGGCTGACTAACGACGCTCCTGAGTACCTGCTCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCa                                                                             >  2:334186/1‑139 (MQ=255)
                                                   gCCGCATTGCTATCGAGTGGCCAGGTAAAGTGGTAGAGGCCATTCTCCGGCTGACTAACGACGCTCCTGAGTACCTGCTCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCAt                                                                            >  2:651657/1‑139 (MQ=255)
                                                     cGCATTGCTATCGAGTGGCCAGGTAAAGTGGTAGAGGCCATTCTCCGGCTGACTAACGACGCTCCTGAGTACCTGCTCAt                                                                                                                                     >  2:510379/1‑80 (MQ=255)
                                                     cGCATTGCTATCGAGTGGCCAGGTAAAGTGGTAGAGGCCATTCTCCGGCTGACTAACGACGCTCCTGAGTACCTGCTCAt                                                                                                                                     <  1:510379/80‑1 (MQ=255)
                                                     cGCATTGCTATCGAGTGGCCAGGTAAAGTGGTAGAGGCCATTCTCCGGCTGACTAACGACGCTCCTGAGTACCTGCTCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCATCa                                                                          <  1:92493/139‑1 (MQ=255)
                                                         ttGCTATCGAGTGGCCAGGTAAAGTGGTTGAGGCCATTCTCCGGCTGACTAACGCCGCTCCTGGGTACCTGCTCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCATCACgca                                                                      <  2:89314/139‑1 (MQ=255)
                                                          tGCTATCGAGTGGCCAGGTAAAGTGGTAGAGGCCATTCTCCGGCTGACTAACGACGCTCCTGAGTACCTGCTCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCATCACgcag                                                                     <  1:334186/139‑1 (MQ=255)
                                                            cTATCGAGTGGCCAGGTAAAGTGGTAGAGGCCATTCTCCGGCTGACTAACGACGCTCCTGAGTACCTGCTCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCATCACgcagca                                                                   <  2:984282/139‑1 (MQ=255)
                                                                 gAGTGGCCAAGTAAAGTGGTAGAGGCCATTCTCCGGCTGACTAACGACGCTCCTGAGTACCTGCTCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCATCGCGCAGCAAACCa                                                              <  2:941318/139‑1 (MQ=255)
                                                                    tGGCCAGGTAAAGTGGTAGAGGCCATTCTCCGGCTGACTAACGACGCTCCTGAGTACCTGCTCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCATCACGCAGCAAACCATTg                                                           >  2:439944/1‑139 (MQ=255)
                                                                      gCCAGGTAAAGTGGTAGAGGCCATTCTCCGGCTGACTAACGACGCTCCTGAGTACCTGCTCATCGGGTTTAATCACGTCTAACTTGATggg                                                                                                         <  1:7952/91‑1 (MQ=255)
                                                                      gCCAGGTAAAGTGGTAGAGGCCATTCTCCGGCTGACTAACGACGCTCCTGAGTACCTGCTCATCGGGTTTAATCACGTCTAACTTGATggg                                                                                                         >  2:7952/1‑91 (MQ=255)
                                                                      gCCAGGTAAAGAGGTAGAGGCCATTCTCCGGCTGACTAACGACGCTCCTGAGTACCTGCTCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGt                                                                                  <  1:619702/114‑1 (MQ=255)
                                                                      gCCAGGTAAAGAGGTAGAGGCCATTCTCCGGCTGACTAACGACGCTCCTGAGTACCTGCTCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGt                                                                                  >  2:619702/1‑114 (MQ=255)
                                                                               aGTGGTAGAGGCCATTCTCCGGCTGACTAACGACGCTCCTGAGTACCTGCTCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCATCACGCAGCAAACCATTGAGGATTACCGt                                                <  1:746071/139‑1 (MQ=255)
                                                                                gTGGTAGAGGCCATTCTCCGGCTGACTAACGACGCTCCTGAGTACCTGCTCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCATCACGCAGCAAACCATTGAGGATTACCGtt                                               >  1:489916/1‑139 (MQ=255)
                                                                                gTGGTAGAGGCCATTCTCCGGCTGACTAACGACGCTCCTGAGTACCTGCTCATCGGGTTTAAGCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCATCACGCAGCAAACCATTGAGGATTACCGtt                                               >  2:660685/1‑139 (MQ=255)
                                                                                     agagGCCATTCTCCGGCTGACTAACGACGCTCCTGAGTACCTGCTCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCATCACGCAGCAAACCATTGAGGATTACCGTTTCAcc                                          >  1:1007814/1‑139 (MQ=255)
                                                                                     agagGCCATTCTCCGGCTGACTAACGACGCTCCTGAGTACCTGCTCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCATCACGCAGCAAACCATTGAGGATTACCGTTTCAcc                                          >  2:546934/1‑139 (MQ=255)
                                                                                        ggCCATTCTCCGGCTGACTAACGACGCTCCTGAGTACCTGCTCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCATCACGCAGCAAACCATTGAGGATTACCGTTTCACCTgg                                       <  2:1007814/139‑1 (MQ=255)
                                                                                          ccATTCTCCGGCTGACTAACGACGCTCCTGAGTACCTGCTCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCATCACGCAGCAAACCATTGAGGATTACCGTTTCACCTGGGc                                     <  1:439944/139‑1 (MQ=255)
                                                                                             ttCTCCGGCTGACTAACGACGCTCCTGAGTACCTGCTCATCGGGTTTAATCCCGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCATCACGCAGCAAACCATTGAGGATTACCGTTTCACCTGGGCGAt                                  <  1:738463/139‑1 (MQ=255)
                                                                                                 ccGGCTGACTAACGACGCTCCTGAGTACCTGCTCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCATCACGCAGCAAACCATTGAGGATTACCGTTTCACCTGGGCGATAAAg                              <  2:158272/139‑1 (MQ=255)
                                                                                                  cGGCTGACTAACGACGCTCCTGAGTACCTGCTCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCATCACGCAGCAAACCATTGAGGATTACCGTTTCACCTGGGCGATAAAGa                             <  2:46041/139‑1 (MQ=255)
                                                                                                            acgacgCTCCTGAGTACCTGCTCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCATCACGCAGCAAACCATTGAGGATTACCGTTTCACCTgg                                       <  1:107253/119‑1 (MQ=255)
                                                                                                            acgacgCTCCTGAGTACCTGCTCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCATCACGCAGCAAACCATTGAGGATTACCGTTTCACCTgg                                       >  2:107253/1‑119 (MQ=255)
                                                                                                                  cTCCTGAGTACCTGCTCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCa                                                                             >  1:178409/1‑75 (MQ=255)
                                                                                                                  cTCCTGAGTACCTGCTCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCa                                                                             <  2:178409/75‑1 (MQ=255)
                                                                                                                  cTCCTGAGTACCTGCTCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCATCACgcagca                                                                   >  2:417977/1‑85 (MQ=255)
                                                                                                                  cTCCTGAGTACCTGCTCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCATCACgcagca                                                                   <  1:417977/85‑1 (MQ=255)
                                                                                                                  cTCCTGAGTACCTGCTCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCATCACGCAGCAAACCATTGAGGATTACCGTTTCACCTGGGCGATAAAGATCGCGTGGGCCaa                >  2:1047432/1‑136 (MQ=255)
                                                                                                                  cTCCTGAGTACCTGCTCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCATCACGCAGCAAACCATTGAGGATTACCGTTTCACCTGGGCGATAAAGATCGCGTGGGCCaa                <  1:1047432/136‑1 (MQ=255)
                                                                                                                  cTCCTGAGTACCTGCTCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCATCACGCAGCAAACCATTGAGGATTACCGTTTCACCTGGGCGATAAAGATCGCGTGGGCCAAACa             >  2:229847/1‑139 (MQ=255)
                                                                                                                      tGAGTACCTGCTCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCATCACGCAGCAAACCATTGAGGATTACCGTTTCACCTGGGCGATAAAGATCGCGTGGGCCAAACATGaa         >  1:147317/1‑139 (MQ=255)
                                                                                                                       gAGTACCTGCTCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCATCACGCAGCAAACCATTGAGGATTACCGTTTCACCTGGGCGATAAAGATCGCGTGGGCCAAACATGaaa        <  1:852860/139‑1 (MQ=255)
                                                                                                                           aCCTGCTCATCGTGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCATCACGCAGCAAACCATTGAGGATTACCGTTTCACCTGGGCGATAAAGATCGCGTGGGCCAAACATGAAAAACt    <  1:651657/139‑1 (MQ=255)
                                                                                                                             cTGCTCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCATCACGCAGCAAACCATTGAGGATTACCGTTTCACCTGGGCGATAAAGATCGCGTGGGCCAAACATGAAAAACTGt  >  1:558477/1‑139 (MQ=255)
                                                                                                                                 |                                                                                                                                      
ATCCGATACTGATTATCGCCCGTGTTAGCGCGAATATGCCACATACCGGTTGCCGCATTGCTATCGAGTGGCCAGGTAAAGTGGTAGAGGCCATTCTCCGGCTGACTAACGACGCTCCTGAGTACCTGCCCATCGGGTTTAATCACGTCTAACTTGATGGGTTGATTGGGCAACGCTTTACCGTCTGCATCACGCAGCAAACCATTGAGGATTACCGTTTCACCTGGGCGATAAAGATCGCGTGGGCCAAACATGAAAAACTGT  >  NC_000913/2650867‑2651130

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A