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
A11 F1 I2 R1 760 67.6 3323148 92.7% 3080558 109.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,824,491 C→T *362* (TAG→TAA)  mltB ← membrane‑bound lytic murein transglycosylase B

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,824,4910CT98.2% 171.1 / ‑4.2 56*362* (TAG→TAA) mltBmembrane‑bound lytic murein transglycosylase B
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base T (24/31);  total (24/32)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.93e-01

TGTCAGTCAAAAATTTATGCCGGACAAGATAGCACTTTCGTCAGGAAGATGGTGTTGGCGTTGCAATTTTACGAGGAGGATTCAGAAAAAAGCTGATTAGCCAGAGGGAAGCTCACGCCCCCCTCTTGTAAATAGCTACTGTACTCGCGCCAGCGCCACGGCTTGTCCTAACTGCCAGACCGCCATTGCGTAATGGGTGCTGTGGTTGTAACGGGTGATGGTGTAGAAGTTCGGCAGACCGTACCAGTACTGGT  >  NC_000913/2824356‑2824609
                                                                                                                                       |                                                                                                                      
tGTCAGTCAAAAATTTATGCCGGACAAGATAGCACTTTCGTCAGGAAGATGGTGTTGGCGTTGCAATTTTACGAGGAGGATTCAGAAAAAAGCTGATTAGCCAGAGGGAAGCTCACGCCCCCCTCTTGTAAATAGTTAc                                                                                                                     >  2:437392/1‑139 (MQ=255)
 gtcagtcaAAAATTTATGCCGGACAAGATAGCACTTTCGTCAGGAAGATGGTGTTGGCGTTGCAATTTTACGAGGAGGATTCAGAAAAAAGCTGATTAGCCAGAGGGAAGCTCACGCCCCCCTCTTGTAAATAGTTACt                                                                                                                    >  2:1186591/1‑139 (MQ=255)
  tcagtcaAAAATTTATGCCGGACAAGATAGCACTTTCGTCAGGAAGATGGTGTTGGCGTTGCAATTTTACGAGGAGGATTCAGAAAAAAGCTGATTAGCCAGAGGGAAGCTCACGCCCCCCTCTTGTAAATAGTTACtt                                                                                                                   >  2:48225/1‑138 (MQ=255)
      tcaAAAATTTATGCCGGACAAGATAGCACTTTCGTCAGGAAGATGGTGTTGGCGTTGCAATTTTACGAGGAGGATTCAGAAAAAAGCTGATTAGCCAGAGGGAAGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTc                                                                                                              >  2:196837/1‑139 (MQ=255)
                      gACAAGATAGCACTTTCGTCAGGAAGATGGTGTTGGCGTTGCAATTTTACGAGGAGGATTCAGAAAAAAGCTGATTAGCCAGAGGGAAGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGc                                                                                              >  2:598531/1‑139 (MQ=255)
                       aCAAGATAGCACTTTCGTCAGGAAGATGGTGTTGGCGTTGCAATTTTACGAGGAGGATTCAGAAAAAAGCTGATTAGCCAGAGGGAAGCTCACGCCCCCCTCTTGTAAATAGCTACTGTACTCGCGCCAGCGCCACGGc                                                                                              <  2:778310/139‑1 (MQ=255)
                             tAGCACTTTCGTCAGGAAGATGGTGTTGGCGTTGCAATTTTACGAGGAGGATTCAGAAAAAAGCTGATTAGCCAGAGGGAAGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGCTTGTCCt                                                                                       <  1:1186591/139‑1 (MQ=255)
                                cACTTTCGTCAGGAAGATGGTGTTGGCGTTGCAATTTTACGAGGAGGATTCAGAAAAAAGCTGATTAGCCAGAGGGAAGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCgcgcca                                                                                                        >  2:495050/1‑119 (MQ=255)
                                cACTTTCGTCAGGAAGATGGTGTTGGCGTTGCAATTTTACGAGGAGGATTCAGAAAAAAGCTGATTAGCCAGAGGGAAGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCgcgcca                                                                                                        <  1:495050/119‑1 (MQ=255)
                                cACTTTCGTCAGGAAGATGGTGTTGGCGTTGCAATTTTACGAGGAGGATTCAGAAAAAAGCTGATTAGCCAGAGGGAAGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGCTTGTCCTAAc                                                                                    <  2:1594309/139‑1 (MQ=255)
                                 aCTTTCGTCAGGAAGATGGTGTTGGCGTTGCAATTTTACGAGGAGGATTCAGAAAAAAGCTGATTAGCCAGAGGGAAGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGCTTGTCCtctgc                                                                                   >  2:473846/1‑135 (MQ=255)
                                 aCTTTCGTCAGGAAGATGGTGTTGGCGTTGCAATTTTACGAGGAGGATTCAGAAAAAAGCTGATTAGCCAGAGGGAAGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGCTTGTCCTAACt                                                                                   <  2:757764/139‑1 (MQ=255)
                                     tCGTCAGGAAGATGGTGTTGGCGTTGCAATTTTACGAGGAGGATTCAGAAAAAAGCTGATTAGCCAGAGGGAAGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGCTTGTCCTAACTGCCa                                                                               >  1:861653/1‑139 (MQ=255)
                                     tCGTCAGGAAGATGGTGTTGGCGTTGCAATTTTACGAGGAGGATTCAGAAAAAAGCTGATTAGCCAGAGGGAAGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGCTTGTCCTAACTGCCa                                                                               >  2:414964/1‑139 (MQ=255)
                                     tCGTCAGGAAGATGGTGTTGGCGTTGCAATTTTACGAGGAGGATTCAGAAAAAAGCTGATTAGCCAGAGGGAAGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGCTTGTCCTAACTGCCa                                                                               >  1:833211/1‑139 (MQ=255)
                                     tCGTCAGGAAGATGGTGTTGGCGTTGCAATTTTACGAGGAGGATTCAGAAAAAAGCTGATTAGCCAGAGGGAAGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGCTTGTCCTAACTGCCa                                                                               >  1:739409/1‑139 (MQ=255)
                                        gcAGGAAGATGGTGTTGGCGTTGCAATTTTACGAGGAGGATTCAGAAAAAAGCTGATTAGCCAGAGGGAAGCTCACGACCCCTTCTTGTAAATAGTTACT‑TACCCGCGCCAGCGCCACGGCTTGTCCTAACTGCCAGAc                                                                            <  1:518641/138‑1 (MQ=255)
                                          aGGAAGATGGTGTTGGCGTTGCAATTTTACGAGGAGGATTCAGAAAAAAGCTGATTAGCCAGAGGGAAGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGCTTGTCCTAACTGCCAGACCg                                                                          <  1:414964/139‑1 (MQ=255)
                                            gAAGATGGTGTTGGCGTTGCAATTTTACGAGGAGGATTCAGAAAAAAGCTGATTAGCCAGAGGGAAGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGCTTGTCCTAACTGCCAGACCGcc                                                                        <  2:739409/139‑1 (MQ=255)
                                             aaGATGGTGTTGGCGTTGCAATTTTACGAGGAGGATTCAGAAAAAAGCTGATTAGCCAGAGGGAAGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGCTTGTCCTAACTGCCAGACCGCCa                                                                       <  2:1151375/139‑1 (MQ=255)
                                              aGATGGTGTTGGCGTTGCAATTTTACGAGGAGGATTCAGAAAAAAGCTGATTAGCCAGAGGGAAGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGCTTGTCCTAACTGCCAGACCGCCAt                                                                      <  1:135003/139‑1 (MQ=255)
                                                      ttGGCGTTGCAATTTTACGAGGAGGATTCAGAAAAAAGCTGATTAGCCAGAGGGAAGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCgcgccagcgcc                                                                                                   <  2:672578/102‑1 (MQ=255)
                                                      ttGGCGTTGCAATTTTACGAGGAGGATTCAGAAAAAAGCTGATTAGCCAGAGGGAAGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCgcgccagcgcc                                                                                                   >  1:672578/1‑102 (MQ=255)
                                                      ttGGCGTTGCAATTTTACGAGGAGGATTCAGAAAAAAGCTGATTAGCCAGAGGGAAGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGCTTGTCCTAACTGCCAGACCGCCATTGCGTAAt                                                              <  1:1194368/139‑1 (MQ=255)
                                                        ggCGTTGCAATTTTACGAGGAGGATTCAGAAAAAAGCTGATTAGCCAGAGGGAAGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGCTTGTCCTAACTGCCAGACCGCCATTGCGTAATgg                                                            <  2:833211/139‑1 (MQ=255)
                                                           gTTGCAATTTTACGAGGAGGATTCAGAAAAAAGCTGATTAGCCAGAGGGAAGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGCTTGTCCTAACTGCCAGACCGCCATTGCGTAATGGGTg                                                         <  1:217222/139‑1 (MQ=255)
                                                            ttGCAATTTTACGAGGAGGATTCAGAAAAAAGCTGATTAGCCAGAGGGAAGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGCTTGTCCTAACTGCCAGACCGCCATTGCGTAATGGGTGc                                                        <  1:1468764/139‑1 (MQ=255)
                                                              gCAATTTTACGAGGAGGATTCAGAAAAAAGCTGATTAGCCAGAGGGAAGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGCTTGTCCTAACTGCCAGACCGCCATTGCGTAATGGGTGCtg                                                      >  1:1198281/1‑139 (MQ=255)
                                                                            aggaTTCAGAAAAAAGCTGATTAGCCAGAGGGAAGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGCTTGTCCTAACTGCCAGACCg                                                                          >  1:872189/1‑105 (MQ=255)
                                                                            aggaTTCAGAAAAAAGCTGATTAGCCAGAGGGAAGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGCTTGTCCTAACTGCCAGACCg                                                                          <  2:872189/105‑1 (MQ=255)
                                                                            aggaTTCAGAAAAAAGCTGATTAGCCAGAGGGAAGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGCTTGTCCT‑‑CTGCCAGACCGCCATTGCGTAATGGGTGCTGTGGTTGTAACGGGTGa                                      <  1:473846/139‑1 (MQ=255)
                                                                              gaTTCAGAAAAAAGCTGATTAGCCAGAGGGAAGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGCTTGTCCTAACTGCCAGACCGCCATTGCGTAATGGGTGCTGTGGTTGTAACGGGTGa                                      <  2:1198281/139‑1 (MQ=255)
                                                                              gaTTCAGAAAAAAGCTGATTAGCCAGAGGGAAGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGCTTGTCCTAACTGCCAGACCGCCATTGCGTAATGGGTGCTGTGGTTGTAACGGGTGa                                      <  1:598531/139‑1 (MQ=255)
                                                                                        aaaGCTGATTAGCCAGAGGGAAGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGCTTGTCCTAACTGCCAGAc                                                                            >  2:189360/1‑91 (MQ=255)
                                                                                        aaaGCTGATTAGCCAGAGGGAAGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGCTTGTCCTAACTGCCAGAc                                                                            <  1:189360/91‑1 (MQ=255)
                                                                                        aaaGCTGATTAGCCAGAGGGAAGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGCTTGTCCTAACTGCCAGACCGCCATTGCGTAATGGGTGCTGTGGTTGTAACGGGTGATGGTGTAGaa                            <  2:861653/139‑1 (MQ=255)
                                                                                        aaaGCTGATTAGCCAGAGGGAAGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGCTTGTCCTAACTGCCAGACCGCCATTGCGTAATGGGTGCTGTGGTTGTAACGGGTGATGGTGTAGaa                            >  1:1462437/1‑139 (MQ=255)
                                                                                               aTTAGCCAGAGGGAAGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGCTTGTCCTAACTGCCAGAc                                                                            >  1:622924/1‑84 (MQ=255)
                                                                                               aTTAGCCAGAGGGAAGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGCTTGTCCTAACTGCCAGAc                                                                            <  2:622924/84‑1 (MQ=255)
                                                                                               aTTAGCCAGAGGGAAGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGCTTGTCCTAACTGCCAGACCGCCATTGCGTAATGGGTGCTGTGGTTGTAACGGGTGAt                                     >  1:651655/1‑123 (MQ=255)
                                                                                               aTTAGCCAGAGGGAAGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGCTTGTCCTAACTGCCAGACCGCCATTGCGTAATGGGTGCTGTGGTTGTAACGGGTGAt                                     <  2:651655/123‑1 (MQ=255)
                                                                                               aTTAGCCAGAGGGAAGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGCTTGTCCTAACTGCCAGACCGCCATTGCGTAATGGGTGCTGTGGTTGTAACGGGTGATGGTGTAGAAGTTCGGc                     >  2:180053/1‑139 (MQ=255)
                                                                                                   gCCAGAGGGAAGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGCTTGTCCTAACTGCCAGACCGCCATTGCGTAATGGGTGCTGTGGTTGTAACGGGTGATGGTGTAGAAGTTCGGCAGAc                 <  1:196837/139‑1 (MQ=255)
                                                                                                   gCCAGAGGGAAGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGCTTGTCCTAACTGCCAGACCGCCATTGCGTAATGGGTGCTGTGGTTGTAACGGGTGATGGTGTAGAAGTTCGGCAGAc                 <  1:48225/139‑1 (MQ=255)
                                                                                                      agagGGAAGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGCTTGTCCTAACTGCCAGACCGCCATTGCGTAATGGGTGCTGTGGTTGTAACGGGTGATGGTGTAGAAGTTCGGCAGAc                 <  2:1509279/136‑1 (MQ=255)
                                                                                                      agagGGAAGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGCTTGTCCTAACTGCCAGACCGCCATTGCGTAATGGGTGCTGTGGTTGTAACGGGTGATGGTGTAGAAGTTCGGCAGAc                 >  1:1509279/1‑136 (MQ=255)
                                                                                                        agGGAAGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGCTTGTCCTAACTGCCAGACCGCCATTGCGTAATGGGTGCTGTGGTTGTAACGGGTGATGGTGTAGAAGTTCGGCAGACCGTAc            <  2:1462437/139‑1 (MQ=255)
                                                                                                        agGGAAGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGCTTGTCCTAACTGCCAGACCGCCATTGCGTAATGGGTGCTGTGGTTGTAACGGGTGATGGTGTAGAAGTTCGGCAGACCGTAc            <  1:1228263/139‑1 (MQ=255)
                                                                                                           gAAGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGCTTGTCCTAACTGCCAGACCGCCATTGCGTAATGGGTGCTGTGGTTGTAACGGGTGATGGTGTAGAAGTTCGGCAGACCGTACCAg         <  1:437392/139‑1 (MQ=255)
                                                                                                             aGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGCTTGTCCTAACTGCCAGACCGCCATTGCGTAATg                                                             >  2:936671/1‑85 (MQ=255)
                                                                                                             aGCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGCTTGTCCTAACTGCCAGACCGCCATTGCGTAATg                                                             <  1:936671/85‑1 (MQ=255)
                                                                                                              gCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGCTTGTCCTAACTGCCAGACCGCCATTGCGTAATGGGTGCTGTGGTTGTAACGGGTGATGGTGTAGAAGTTCGGCAGa                  <  1:890455/127‑1 (MQ=255)
                                                                                                              gCTCACGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGCTTGTCCTAACTGCCAGACCGCCATTGCGTAATGGGTGCTGTGGTTGTAACGGGTGATGGTGTAGAAGTTCGGCAGa                  >  2:890455/1‑127 (MQ=255)
                                                                                                                  aCGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGCTTGTCCTAACTGCCAGACCGCCATTGCGTAATGGGTGCTGTGGTTGTAACGGGTGATGGTGTAGAAGTTCGGCAGACCGTa             >  2:195379/1‑128 (MQ=255)
                                                                                                                  aCGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGCTTGTCCTAACTGCCAGACCGCCATTGCGTAATGGGTGCTGTGGTTGTAACGGGTGATGGTGTAGAAGTTCGGCAGACCGTa             <  1:195379/128‑1 (MQ=255)
                                                                                                                  aCGCCCCCCTCTTGTAAATAGTTACT‑TACTCGCGCCAGCGCCACGGCTTGTCCTAACTGCCAGACCGCCATTGCGTAATGGGTGCTGTGGTTGTAACGGGTGATGGTGTAGAAGTTCGGCAGACCGTACCAGTACTGGt  >  1:363711/1‑139 (MQ=255)
                                                                                                                                       |                                                                                                                      
TGTCAGTCAAAAATTTATGCCGGACAAGATAGCACTTTCGTCAGGAAGATGGTGTTGGCGTTGCAATTTTACGAGGAGGATTCAGAAAAAAGCTGATTAGCCAGAGGGAAGCTCACGCCCCCCTCTTGTAAATAGCTACTGTACTCGCGCCAGCGCCACGGCTTGTCCTAACTGCCAGACCGCCATTGCGTAATGGGTGCTGTGGTTGTAACGGGTGATGGTGTAGAAGTTCGGCAGACCGTACCAGTACTGGT  >  NC_000913/2824356‑2824609

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A