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 F50 I2 R1 104 44.1 1376607 98.9% 1361464 150.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,089,445 (G)5→4 coding (413/2019 nt) pgaB ← poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine (PGA) N‑deacetylase outer membrane export lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,089,4410G.97.7% 205.9 / ‑1.6 44coding (417/2019 nt)pgaBpoly‑beta‑1,6‑N‑acetyl‑D‑glucosamine (PGA) N‑deacetylase outer membrane export lipoprotein
Reads supporting (aligned to +/- strand):  ref base G (0/1);  new base . (23/20);  total (23/21)
Fisher's exact test for biased strand distribution p-value = 4.77e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

GAGAATTCCATGTATGAGAAGCGAGCTCAACGAGCCGGGAACGCGCAACTTCTCGCACTTGTTGCCACGTGGCAAAATATTCTCGATCGACCAACTCATCGCCAAATTTTACTTGTTTATCCGCTGGCGTATCGACCCAACTGCCGACGGGGGCCCATACAGCAGGCCACTGGAAGGCCTGAAGAATTGGGAAGACGCGGGTATAAAAACTCTGGTAGCCGTCATCAAAAGTCAGCACTACAGCTTTTTCCGGTAGCGGTTTTCCTCCTCGATGTGCTTCACGAATTTGAGCAAT  >  NC_000913/1089293‑1089587
                                                                                                                                                    |                                                                                                                                                  
gagaATTCCATGTATGAGAAGCGAGCTCAACGAGCCGGGAACGCGCAACTTCTCGCACTTGTTGCCACGTGGCAAAATATTCTCGATCGACCAACTCATCGCCAAATTTTACTTGTTTATCCGCTGGCGTATCGACCCAACTGCCGACggg                                                                                                                                                  <  2:558967/151‑1 (MQ=255)
gagaATTCCATGTATGAGAAGCGAGCTCAACGAGCCGGGAACGCGCAACTTCTCGCACTTGTTGCCACGTGGCAAAATATTCTCGATCGACCAACTCATCGCCAAATTTTACTTGTTTATCCGCTGGCGTATCGACCCAACTGCCGACggg                                                                                                                                                  >  2:633438/1‑151 (MQ=255)
 agaATTCCATGTATGAGAAGCGAGCTCAACGAGCCGGGAACGCGCAACTTCTCGCACTTGTTGCCACGTGGCAAAATATTCTCGATCGACCAACTCATCGCCAAATTTTACTTGTTTATCCGCTGGCGTATCGACCCAACTGCCGACgggg                                                                                                                                                 >  1:601311/1‑151 (MQ=255)
  gaATTCCATGTATGAGAAGCGAGCTCAACGAGCCGGGAACGCGCAACTTCTCGCACTTGTTGCCACGTGGCAAAATATTCTCGATCGACCAACTCATCGCCAAATTTTACTTGTTTATCCGCTGGCGTATCGACCCAACTGCCGACggggc                                                                                                                                                >  1:56604/1‑150 (MQ=255)
       ccATGTATGAGAAGCGAGCTCAACGAGCCGGGAACGCGCAACTTCTCGCACTTGTTGCCACGTGGCAAAATATTCTCGATCGACCAACTCATCGCCAAATTTTACTTGTTTATCCGCTGGCGTATCGACCCAACTGCCGACGGGGccca                                                                                                                                             <  1:319676/149‑2 (MQ=255)
       ccATGTATGAGAAGCGAGCTCAACGAGCCGGGAACGCGCAACTTCTCGCACTTGTTGCCACGTGGCAAAATATTCTCGATCGACCAACTCATCGCCAAATTTTACTTGTTTATCCGCTGGCGTATCGACCCAACTGCCGAC‑GGGGCCCAt                                                                                                                                           >  1:556798/1‑150 (MQ=255)
          tGTATGAGAAGCGAGCTCAACGAGCCGGGAACGCGCAACTTCTCGCACTTGTTGCCACGTGGCAAAATATTCTCGATCGACCAACTCATCGCCAAATTTTACTTGTTTATCCGCTGGCGTATCGACCCAACTGCCGAC‑GGGGCCCATAc                                                                                                                                         >  2:430877/1‑149 (MQ=255)
                    gCGAGCTCAACGAGCCGGGAACGCGCAACTTCTCGCACTTGTTGCCACGTGGCAAAATATTCTCGATCGACCAACTCATCGCCAAATTTTACTTGTTTATCCGCTGGCGTATCGACCCAACTGCCGAC‑GGGGCCCATACAGCAGGCCACTg                                                                                                                             >  1:632484/1‑151 (MQ=255)
                      gAGCTCAACGAGCCGGGAACGCGCAACTTCTCGCACTTGTTGCCACGTGGCAAAATATTCTCGATCGACCAACTCATCGCCAAATTTTACTTGTTTATCCGCTGGCGTATCGACCCAACTGCCGAC‑GGGGCCCATACAGCAGGCCACTgg                                                                                                                            >  1:486189/1‑150 (MQ=255)
                          tCAACGAGCCGGGAACGCGCAACTTCTCGCACTTGTTGCCACGTGGCAAAATATTCTCGATCGACCAACTCATCGCCAAATTTTACTTGTTTATCCGCTGGCGTATCGACCCAACTGCCGAC‑GGGGCCCATACAGCAGGCCACTGGAAGGc                                                                                                                       >  2:636375/1‑151 (MQ=255)
                            aaCGAGCCGGGAACGCGCAACTTCTCGCACTTGTTGCCACGTGGCAAAATATTCTCGATCGACCAACTCATCGCCAAATTTTACTTGTTTATCCGCTGGCGTATCGACCCAACTGCCGAC‑GGGGCCCATACAGCAGGCCACTGGAAGGCCt                                                                                                                     >  2:421042/1‑151 (MQ=255)
                                 gCCGGGAACGCGCAACTTCTCGCACTTGTTGCCACGTGGCAAAATATTCTCGATCGACCAACTCATCGCCAAATTTTACTTGTTTATCCGCTGGCGTATCGACCCAACTGCCGAC‑GGGGCCCATACAGCAGGCCACTGGAAGGCCTgaaga                                                                                                                <  2:643003/151‑1 (MQ=255)
                                  ccGGGAACGCGCAACTTCTCGCACTTGTTGCCACGTGGCAAAATATTCTCGATCGACCAACTCATCGCCAAATTTTACTTGTTTATCCGCTGGCGTATCGACCCAACTGCCGAC‑GGGGCCCATACAGCAGGCCACTGGAAGGCCTgaagaa                                                                                                               <  2:323883/151‑1 (MQ=255)
                                         cgcgCAACTTCTCGCACTTGTTGCCACGTGGCAAAATATTCTCGATCGACCAACTCATCGCCAAATTTTACTTGTTTATCCGCTGGCGTATCGACCCAACTGCCGAC‑GGGGCCCATACAGCAGGCCACTGGAAGGCCTGAAGAATTGGGaa                                                                                                        <  2:350301/151‑1 (MQ=255)
                                         cgcgCAACTTCTCGCACTTGTTGCCACGTGGCAAAATATTCTCGATCGACCAACTCATCGCCAAATTTTACTTGTTTATCCGCTGGCGTATCGACCCAACTGCCGAC‑GGGGCCCATACAGCAGGCCACTGGAAGGCCTGAAGAATTGGGa                                                                                                         >  1:103051/1‑150 (MQ=255)
                                          gcgcAACTTCTCGCACTTGTTGCCACGTGGCAAAATATTCTCGATCGACCAACTCATCGCCAAATTTTACTTGTTTATCCGCTGGCGTATCGACCCAACTGCCGAC‑GGGGCCCATACAGCAGGCCACTGGAAGGCCTGAAGAATTGGGAAg                                                                                                       <  1:451369/151‑1 (MQ=255)
                                            gcAACTTCTCGCACTTGTTGCCACGTGGCAAAATATTCTCGATCGACCAACTCATCGCCAAATTTTACTTGTTTATCCGCTGGCGTATCGACCCAACTGCCGAC‑GGGGCCCATACAGCAGGCCACTGGAAGGCCTGAAGAATTGGGAAGAc                                                                                                     >  2:341896/1‑151 (MQ=255)
                                               aCTTCTCGCACTTGTTGCCACGTGGCAAAATATTCTCGATCGACCAACTCATCGCCAAATTTTACTTGTTTATCCGCTGGCGTATCGACCCAACTGCCGAC‑GGGGCCCATACAGCAGGCCACTGGAAGGCCTGAAGAATTGGGAAGAcgcg                                                                                                  >  2:471484/1‑151 (MQ=255)
                                                    tcGCACTTGTTGCCACGTGGCAAAATATTCTCGATCGACCAACTGATCGCCAAATTTTACTTGTTTATCCGCTGGCGTATCGACCCAACTGCCGAC‑GGGGCCCATACAGCAGGCCACTGGAAGGCCTGAAGAATTGGGAAGACGCGGGtat                                                                                             >  2:500373/1‑151 (MQ=255)
                                                     cGCACTTGTTGCCACGTGGCAAAATATTCTCGATCGACCAACTCATCGCCAAATTTTACTTGTTTATCCGCTGGCGTATCGACCCAACTGCCGAC‑GGGGCCCATACAGCAGGCCACTGGAAGGCCTGAAGAATTGGGAAGACGCGGGtata                                                                                            <  1:293484/151‑1 (MQ=255)
                                                                 cACGTGGCAAAATATTCTCGATCGACCAACTCATCGCCAAATTTTACTTGTTTATCCGCTGGCGTATCGACCCAACTGCCGAC‑GGGGCCCATACAGCAGGCCACTGGAAGGCCTGAAGAATTGGGAAGACGCGGGTATAAAAACTCTGGTa                                                                                <  2:382268/151‑1 (MQ=255)
                                                                     tGGCAAAATATTCTCGATCGACCAACTCATCGCCAAATTTTACTTGTTTATCCGCTGGCGTATCGACCCAACTGCCGAC‑GGGGCCCATACAGCAGGCCACTGGAAGGCCTGAAGAATTGGGAAGACGCGGGTATAAAAACTCTGGTAGCCg                                                                            >  2:591476/1‑151 (MQ=255)
                                                                        cAAAATATTCTCGATCGACCAACTCATCGCCAAATTTTACTTGTTTATCCGCTGGCGTATCGACCCAACTGCCGAC‑GGGGCCCATACAGCAGGCCACTGGAAGGCCTGAAGAATTGGGAAGACGCGGGTATAAAAACTCTGGTAGCCGtca                                                                         <  2:674705/151‑1 (MQ=255)
                                                                         aaaaTATTCTCGATCGACCAACTCATCGCCAAATTTTACTTGTTTATCCGCTGGCGTATCGACCCAACTGCCGAC‑GGGGCCCATACAGCAGGCCACTGGAAGGCCTGAAGAATTGGGAAGACGCGGGTATAAAAACTCTGGTAGCCGtcat                                                                        <  1:555750/151‑1 (MQ=255)
                                                                             tatTCTCGATCGACCAACTCATCGCCAAATTTTACTTGTTTATCCGCTGGCGTATCGACCCAACTGCCGAC‑GGGGCCCATACAGCAGGCCACTGGAAGGCCTGAAGAATTGGGAAGACGCGGGTATAAAAACTCTGGTAGCCGTCATCaa                                                                     >  2:499322/1‑150 (MQ=255)
                                                                                   cgatcgaCCAACTCATCGCCAAATTTTACTTGTTTATCCGCTGGCGTATCGACCCAACTGCCGAC‑GGGGCCCATACAGCAGGCCACTGGAAGGCCTGAAGAATTGGGAAGACGCGGGTATAAAAACTCTGGTAGCCGTCATCAAAAGTCa                                                               <  1:449572/150‑1 (MQ=255)
                                                                                     atcgaCCAACTCATCGCCAAATTTTACTTGTTTATCCGCTGGCGTATCGACCCAACTGCCGAC‑GGGGCCCATACAGCAGGCCACTGGAAGGCCTGAAGAATTGGGAAGACGCGGGTATAAAAACTCTGGTAGCCGTCATCAAAAGTCAGc                                                             >  2:633638/1‑150 (MQ=255)
                                                                                      tcgaCCAACTCATCGCCAAATTTTACTTGTTTATCCGCTGGCGTATCGACCCAACTGCCGAC‑GGGGCCCATACAGCAGGCCACTGGAAGGCCTGAAGAATTGGGAAGACGCGGGTATAAAAACTCTGGTAGCCGTCATCAAAAGTCAGCAc                                                           >  2:629701/1‑151 (MQ=255)
                                                                                      tcgaCCAACTCATCGCCAAATTTTACTTGTTTATCCGCTGGCGTATCGACCCAACTGCCGAC‑GGGGCCCATACAGCAGGCCACTGGAAGGCCTGAAGAATTGGGAAGACGCGGGTATAAAAACTCTGGTAGCCGTCATCAAAAGTCAGCAc                                                           >  1:593522/1‑151 (MQ=255)
                                                                                       cgaCCAACTCATCGCCAAATTTTACTTGTTTATCCGCTGGCGTATCGACCCAACTGCCGAC‑GGGGCCCATACAGCAGGCCACTGGAAGGCCTGAAGAATTGGGAAGACGCGGGTATAAAAACTCTGGTAGCCGTCATCAAAAGTCAGCACt                                                          >  2:595751/1‑151 (MQ=255)
                                                                                         aCCAACTCATCGCCAAATTTTACTTGTTTATCCGCTGGCGTATCGACCCAACTGCCGAC‑GGGGCCCATACAGCAGGCCACTGGAAGGCCTGAAGAATTGGGAAGACGCGGGTATAAAAACTCTGGTAGCCGTCATCAAAAGTCAGCACTa                                                         <  1:406352/150‑1 (MQ=255)
                                                                                          ccAACTCATCGCCAAATTTTACTTGTTTATCCGCTGGCGTATCGACCCAACTGCCGAC‑GGGGCCCATACAGCAGGCCACTGGAAGGCCTGAAGAATTGGGAAGACGCGGGTATAAAAACTCTGGTAGCCGTCATCAAAAGTCAGCACTACa                                                       <  1:533271/151‑1 (MQ=255)
                                                                                           cAACTCATCGCCAAATTTTACTTGTTTATCCGCTGGCGTATCGACCCAACTGCCGAC‑GGGGCCCATACAGCAGGCCACTGGAAGGCCTGAAGAATTGGGAAGACGCGGGTATAAAAACTCTGGTAGCCGTCATCAAAAGTCAGCACTACAg                                                      <  1:198119/151‑1 (MQ=255)
                                                                                            aaCTCATCGCCAAATTTTACTTGTTTATCCGCTGGCGTATCGACCCAACTGCCGAC‑GGGGCCCATACAGCAGGCCACTGGAAGGCCTGAAGAATTGGGAAGACGCGGGTATAAAAACTCTGGTAGCCGTCATCAAAAGTCAGCACTACAGc                                                     <  1:622048/151‑1 (MQ=255)
                                                                                                 aTCGCCAAATTTTACTTGTTTATCCGCTGGCGTATCGACCCAACTGCCGAC‑GGGGCCCATACAGCAGGCCACTGGAAGGCCTGAAGAATTGGGAAGACGCGGGTATAAAAACTCTGGTAGCCGTCATCAAAAGTCAGCACTACAGCttttt                                                <  2:200141/151‑1 (MQ=255)
                                                                                                    gCCAAATTTTACTTGTTTATCCGCTGGCGTATCGACCCAACTGCCGAC‑GGGGCCCATACAGCAGGCCACTGGAAGGCCTGAAGAATTGGGAAGACGCGGGTATAAAAACTCTGGTAGCCGTCATCAAAAGTCAGCACTACAGCTTTTTCCg                                             >  2:405847/1‑151 (MQ=255)
                                                                                                     ccAAATTTTACTTGTTTATCCGCTGGCGTATCGACCCAACTGCCGAC‑GGGGCCCATACAGCAGGCCACTGGAAGGCCTGAAGAATTGGGAAGACGCGGGTATAAAAACTCTGGTAGCCGTCATCAAAAGTCAGCACTACAGCTTTTTCCgg                                            <  1:279901/151‑1 (MQ=255)
                                                                                                           tttACTTGTTTATCCGCTGGCGTATCGACCCAACTGCCGAC‑GGGGCCCATACAGCAGGCCACTGGAAGGCCTGAAGAATTGGGAAGACGCGGGTATAAAAACTCTGGTAGCCGTCATCAAAAGTCAGCACTACAGCTTTTTCCGGTAGCgg                                      >  2:663263/1‑151 (MQ=255)
                                                                                                           tttACTTGTTTATCCGCTGGCGTATCGACCCAACTGCCGAC‑GGGGCCCATACAGCAGGCCACTGGAAGGCCTGAAGAATTGGGAAGACGCGGGTATAAAAACTCTGGTAGCCGTCATCAAAAGTCAGCACTACAGCTTTTTCCGGTAGCg                                       <  2:184946/150‑1 (MQ=255)
                                                                                                                  gTTTATCCGCTGGCGTATCGACCCAACTGCCGAC‑GGGGCCCATACAGCAGGCCACTGGAAGGCCTGAAGAATTGGGAAGACGCGGGTATAAAAACTCTGGTAGCCGTCATCAAAAGTCAGCACTACAGCTTTTTCCGGTAGCGGTTTtcct                               >  1:682609/1‑151 (MQ=255)
                                                                                                                      aTCCGCTGGCGTATCGACCCAACTGCCGAC‑GGGGCCCATACAGCAGGCCACTGGAAGGCCTGAAGAATTGGGAAGACGCGGGTATAAAAACTCTGGTAGCCGTCATCAAAAGTCAGCACTACAGCTTTTTCCGGTAGCGGTTTTCctcctc                           >  2:627918/1‑151 (MQ=255)
                                                                                                                                gTATCGACCCAACTGCCGAC‑GGGGCCCATACAGCAGGCCACTGGAAGGCCTGAAGAATTGGGAAGACGCGGGTATAAAAACTCTGGTAGCCGTCATCAAAAGTCAGCACTACAGCTTTTTCCGGTAGCGGTTTTCCTCCTCGATGTGCTTc                 <  2:217934/151‑1 (MQ=255)
                                                                                                                                  aTCGACCCAACTGCCGAC‑GGGGCCCATACAGCAGGCCACTGGAAGGCCTGAAGAATTGGGAAGACGCGGGTATAAAAACTCTGGTAGCCGTCATCAAAAGTCAGCACTACAGCTTTTTCCGGTAGCGGTTTTCCTCCTCGATGTGCTTCa                <  1:588169/150‑1 (MQ=255)
                                                                                                                                    cGACCCAACTGCCGAC‑GGGGCCCATACAGCAGGCCACTGGAAGGCCTGAAGAATTGGGAAGACGCGGGTATAAAAACTCTGGTAGCCGTCATCAAAAGTCAGCACTACAGCTTTTTCCGGTAGCGGTTTTCCTCCTCGATGTGCTTCACg              <  2:267855/150‑1 (MQ=255)
                                                                                                                                    cGACCCAACTGCCGAC‑GGGGCCCATACAGCAGGCCACTGGAAGGCCTGAAGAATTGGGAAGACGCGGGTATAAAAACTCTGGTAGCCGTCATCAAAAGTCAGCACTACAGCTTTTTCCGGTAGCGGTTTTCCTCCTCGATGTGCTTCACg              >  2:207616/1‑150 (MQ=255)
                                                                                                                                     gACCCAACTGCCGAC‑GGGGCCCATACAGCAGGCCACTGGAAGGCCTGAAGAATTGGGAAGACGCGGGTATAAAAACTCTGGTAGCCGTCATCAAAAGTCAGCACTACAGCTTTTTCCGGTAGCGGTTTTCCTCCTCGATGTGCTTCACGaa            <  1:480432/151‑1 (MQ=255)
                                                                                                                                              gCCGAC‑GGGGCCCATACAGCAGGCCACTGGAAGGCCTGAAGAATTGGGAAGACGCGGGTATAAAAACTCTGGTAGCCGTCATCAAAAGTCAGCACTACAGCTTTTTCCGGTAGCGGTTTTCCTCCTCGATGTGCTTCACGAATTTGAGCa    >  2:600100/1‑150 (MQ=255)
                                                                                                                                               ccGAC‑GGGGCCCATACAGCAGGCCACTGGAAGGCCTGAAGAATTGGGAAGACGCGGGTATAAAAACTCTGGTAGCCGTCATCAAAAGTCAGCACTACAGCTTTTTCCGGTAGCGGTTTTCCTCCTCGATGTGCTTCACGAATTTGAGCAAt  >  2:451630/1‑151 (MQ=255)
                                                                                                                                                    |                                                                                                                                                  
GAGAATTCCATGTATGAGAAGCGAGCTCAACGAGCCGGGAACGCGCAACTTCTCGCACTTGTTGCCACGTGGCAAAATATTCTCGATCGACCAACTCATCGCCAAATTTTACTTGTTTATCCGCTGGCGTATCGACCCAACTGCCGACGGGGGCCCATACAGCAGGCCACTGGAAGGCCTGAAGAATTGGGAAGACGCGGGTATAAAAACTCTGGTAGCCGTCATCAAAAGTCAGCACTACAGCTTTTTCCGGTAGCGGTTTTCCTCCTCGATGTGCTTCACGAATTTGAGCAAT  >  NC_000913/1089293‑1089587

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A