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
A7 F1 I1 R1 776 60.0 3074904 90.1% 2770488 104.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,146,011 C→T *195* (TAG→TAA)  yceF ← m(7)GTP pyrophosphatase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,146,0110CT98.4% 199.3 / NA 62*195* (TAG→TAA) yceFm(7)GTP pyrophosphatase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base T (33/28);  minor base G (0/1);  total (33/29)
Fisher's exact test for biased strand distribution p-value = 4.68e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCGTAACGCGCGCTAATACAAGCATATAAACCTGATAATGGGCGGTTGGCCTGATAAGGCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAACTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGT‑‑AAACCAACCAGCGTGTTAGGATCACGCCCCTCTAAACGCTCAAACAGCGTAATGCCAAATCCTTCACTC  >  NC_000913/1145884‑1146140
                                                                                                                               |                                                                                                                                   
gCGTAACGCGCGCTAATACAAGCATATAAACCTGATAATGGGCGGTTGGCCTGATAAGGCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAg                                                                                                                          >  2:738924/1‑139 (MQ=255)
     aCGCGCGCTAATACAAGCATATAAACCTGATAATGGGCGGTTGGCCTGATAAGGCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGt                                                                                                                     <  2:1389200/139‑1 (MQ=255)
                tACAAGCATATAAACCTGATAATGGGCGGTTGGCCTGATAAGGCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTttcccttcc                                                                                                          <  1:738924/139‑1 (MQ=255)
                     gCATATAAACCTGATAATGGGCGGTTGGCCTGATAAGGCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACg                                                                                                     >  1:136873/1‑139 (MQ=255)
                     gCATATAAACCTGATAATGGGCGGTTGGCCTGATAAGGCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACg                                                                                                     >  2:1076309/1‑139 (MQ=255)
                       atatAAACCTGATAATGGGCGGTTGGCCTGATAAGGCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTa                                                                                                   <  1:125931/139‑1 (MQ=255)
                       atatAAACCTGATAATGGGCGGTTGGCCTGATAAGGCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTa                                                                                                   >  2:125931/1‑139 (MQ=255)
                       atatAAACCTGATAATGGGCGGTTGGCCTGATAAGGCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTa                                                                                                   >  2:659175/1‑139 (MQ=255)
                         ataAACCTGATAATGGGCGGTTGGCCTGATAAGGCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTa                                                                                                   <  2:1498821/137‑1 (MQ=255)
                         ataAACCTGATAATGGGCGGTTGGCCTGATAAGGCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTa                                                                                                   >  1:1498821/1‑137 (MQ=255)
                         ataAACCTGATAATGGGCGGTTGGCCTGATAAGGCGTTTACGCCGCATCAGGCCGCAAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAAc                                                                                                 >  1:1482552/1‑139 (MQ=255)
                                 gATAATGGGCGGTTGGCCTGATAAGGCGTTTACGCCGCATCAGGTCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGaca                                                                                         >  1:1173176/1‑139 (MQ=255)
                                  aTAATGGGCGGTCGGCCTGATAAGGCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGacac                                                                                        >  2:554027/1‑139 (MQ=255)
                                      tGGGCGGTTGGCCTGATAAGGCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAgcg                                                                                    >  1:99093/1‑139 (MQ=255)
                                        ggCGGTTGGCCTGATAAGGCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTa                                                                                                   >  2:582595/1‑122 (MQ=255)
                                        ggCGGTTGGCCTGATAAGGCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTa                                                                                                   <  1:582595/122‑1 (MQ=255)
                                        ggCGGTTGGCCTGATAAGGCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGcgcg                                                                                  >  1:1096167/1‑139 (MQ=255)
                                        ggCGGTTGGCCTGATAAGGCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGcgcg                                                                                  >  2:1158001/1‑139 (MQ=255)
                                          cGGTTGGCCTGATAAGGCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGAt                                                                                <  2:99093/139‑1 (MQ=255)
                                               ggCCTGATAAGGCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCg                                                                           >  1:1377905/1‑139 (MQ=255)
                                                        aGGCGTTTACGCCGCATCAGGTCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGT‑‑Aaaccaa                                                                <  2:1173176/139‑1 (MQ=255)
                                                           cGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGT‑‑AAaccaacca                                                             <  1:148125/139‑1 (MQ=255)
                                                           cGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGT‑‑AAaccaacca                                                             <  1:659175/139‑1 (MQ=255)
                                                            gTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGT‑‑AAACCAACCAg                                                            <  1:1076309/139‑1 (MQ=255)
                                                                    cgcATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAg                                                                                                                          >  2:1390954/1‑71 (MQ=255)
                                                                    cgcATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAg                                                                                                                          <  1:1390954/71‑1 (MQ=255)
                                                                    cgcATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGT‑‑AAACCAACCAGCGTGTTAg                                                    >  2:1348121/1‑139 (MQ=255)
                                                                     gcATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGT‑‑AAACCAACCAGCGTGTTAgg                                                   >  1:1153178/1‑139 (MQ=255)
                                                                       aTCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTttcccttccc                                                                                                         <  1:1435568/85‑1 (MQ=255)
                                                                       aTCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTttcccttccc                                                                                                         >  2:1435568/1‑85 (MQ=255)
                                                                            gccgccAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTttcccttc                                                                                                           <  1:94400/78‑1 (MQ=255)
                                                                            gccgccAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTttcccttc                                                                                                           >  2:94400/1‑78 (MQ=255)
                                                                                ccAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTa                                                                                                   <  1:172946/82‑1 (MQ=255)
                                                                                ccAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTa                                                                                                   >  2:172946/1‑82 (MQ=255)
                                                                                 cAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGc                                                                                                                         >  2:1196510/1‑59 (MQ=255)
                                                                                 cAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGc                                                                                                                         <  1:1196510/59‑1 (MQ=255)
                                                                                   gCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAAGTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGT‑‑AAACCAACCAGCGTGTTAGGATCACGCCCCTCTa                                     <  2:1153178/139‑1 (MQ=255)
                                                                                     aCCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGT‑‑AAACCAACCAGCGTGTTAGGATCACGCCCCTCTaaa                                   <  2:136873/139‑1 (MQ=255)
                                                                                      ccGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGTAAAAACCAACCAGCGTGTTAGGATCACGCCCCTCTaa                                    >  2:813582/1‑139 (MQ=255)
                                                                                      ccGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGT‑‑AAACCAACCAGCGTGTTAGGATCACg                                             <  1:1292648/128‑1 (MQ=255)
                                                                                      ccGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGT‑‑AAACCAACCAGCGTGTTAGGATCACg                                             >  2:1292648/1‑128 (MQ=255)
                                                                                        gATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGT‑‑AAACCAACCAGCGTGTTAGGATCACGCCCCTCTAAACGc                                <  1:1348121/139‑1 (MQ=255)
                                                                                        gATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGT‑‑AAACCAACCAGCGTGTTAGGATCACGCCCCTCTAAACGc                                <  1:1132037/139‑1 (MQ=255)
                                                                                         aTTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGT‑‑AAaccaacca                                                             <  1:458477/109‑1 (MQ=255)
                                                                                         aTTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGT‑‑AAaccaacca                                                             >  2:458477/1‑109 (MQ=255)
                                                                                                 aTGCGACGTAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTCTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGT‑‑AAACCAACAAGCGTGTTAGGATCACGCCCCTCTAAACGCTCAAACAGc                       >  2:1454726/1‑139 (MQ=255)
                                                                                                         tAACCACATCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGT‑‑AAACCAACCAGCGTGTTAGGATCACGCCCCTCTAAACGCTAAAACAGCGTAATGcc               <  1:1158001/139‑1 (MQ=255)
                                                                                                                 tCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTa                                                                                                   <  2:555779/49‑1 (MQ=255)
                                                                                                                 tCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTa                                                                                                   >  1:555779/1‑49 (MQ=255)
                                                                                                                 tCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGT‑‑AAACCAACCAGCGTGTTAGGATCACg                                             <  1:1325681/101‑1 (MQ=255)
                                                                                                                 tCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGT‑‑AAACCAACCAGCGTGTTAGGATCACg                                             >  2:1325681/1‑101 (MQ=255)
                                                                                                                 tCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGT‑‑AAACCAACCAGCGTGTTAGGATCACGCCCCTCTAAACGCTCaa                            <  2:1155174/118‑1 (MQ=255)
                                                                                                                 tCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGT‑‑AAACCAACCAGCGTGTTAGGATCACGCCCCTCTAAACGCTCaa                            >  1:1155174/1‑118 (MQ=255)
                                                                                                                 tCCGGCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGT‑‑AAACCAACCAGCGTGTTAGGATCACGCCCCTCTAAACGCTCAAACAGCGTAATGCCAAATCCtt       <  1:81058/139‑1 (MQ=255)
                                                                                                                    ggCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCg                                                                           <  2:176005/70‑1 (MQ=255)
                                                                                                                    ggCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCg                                                                           >  1:176005/1‑70 (MQ=255)
                                                                                                                    ggCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGt                                                                         <  2:521336/72‑1 (MQ=255)
                                                                                                                    ggCGCAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGt                                                                         >  1:521336/1‑72 (MQ=255)
                                                                                                                     gcgcAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGT‑‑AAACCAACCAGCGTGTTAGGATCACGCCCCTCTAAACGCTCAAACAGCGTAATGCCAAATCCTTCAct   >  1:1150332/1‑139 (MQ=255)
                                                                                                                      cgcAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACg                                                                                                     >  2:530328/1‑42 (MQ=255)
                                                                                                                      cgcAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACg                                                                                                     <  1:530328/42‑1 (MQ=255)
                                                                                                                      cgcAAAAAATTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGT‑‑AAACCAACCAGCGTGTTAGGATCACGCCCCTCTAAACGCTCAAACAGCGTAATGCCAAATCCTTCActc  >  2:96328/1‑139 (MQ=255)
                                                                                                                               |                                                                                                                                   
GCGTAACGCGCGCTAATACAAGCATATAAACCTGATAATGGGCGGTTGGCCTGATAAGGCGTTTACGCCGCATCAGGCCGCCAGCACCGATTGCCGGATGCGACGTAACCACATCCGGCGCAAAAAACTATCCCATCAGCGGGTTTTTCCCTTCCCGACGTAACATCTGACACAGCGCGATTAGCGGT‑‑AAACCAACCAGCGTGTTAGGATCACGCCCCTCTAAACGCTCAAACAGCGTAATGCCAAATCCTTCACTC  >  NC_000913/1145884‑1146140

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