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
A2 F1 I2 R1 78 65.3 3016648 94.6% 2853749 111.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,606,330 (G)8→9 noncoding (72/87 nt) leuQ ← tRNA‑Leu

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,606,3221.G95.8% 157.7 / 0.2 48noncoding (80/87 nt)leuQtRNA‑Leu
Reads supporting (aligned to +/- strand):  ref base . (1/1);  new base G (25/21);  total (26/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.42e-01

TTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGC‑GA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGT  >  NC_000913/4606184‑4606453
                                                                                                                                            |                                                                                                                                   
ttGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGC‑Ga                                                                                                                                      >  2:822210/1‑139 (MQ=255)
       cGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGC‑GA‑ggggggg                                                                                                                              >  1:1322828/1‑139 (MQ=255)
                    gCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGC‑GAGGGGGGGGGACTTGAAcccc                                                                                                                  >  1:1484784/1‑139 (MQ=255)
                          ggggggACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGC‑GAGGGGGGGGGACTTGAACCCCCACGTc                                                                                                            <  1:822210/139‑1 (MQ=255)
                             gggACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGC‑GAGGGGGGGGGACTTGAACCCCCACGTCCGt                                                                                                         >  2:1132787/1‑139 (MQ=255)
                               gACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGC‑GAGGGGGGGGGACTTGAACCCCCACGTCCGTaa                                                                                                       <  1:195600/139‑1 (MQ=255)
                                 cTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCGCCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGC‑GAGGGGGGGGGTATTGGACCCCCACGCCCGTCAgg                                                                                                     >  2:1040750/1‑139 (MQ=21)
                                  ttGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGC‑GAGGGGGGGGGACTTGAACCCCCACGTCCGTa                                                                                                        >  2:389187/1‑135 (MQ=255)
                                  ttGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGC‑GAGGGGGGGGGACTTGAACCCCCACGTCCGTa                                                                                                        <  1:389187/135‑1 (MQ=255)
                                    gAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGC‑GAGGGGGGGGGACTTGaa                                                                                                                      <  1:831406/119‑1 (MQ=255)
                                    gAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGC‑GAGGGGGGGGGACTTGaa                                                                                                                      >  2:831406/1‑119 (MQ=255)
                                    gAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGC‑GAGGGGGGGGGACTTGAACCCCCa                                                                                                                >  2:1369569/1‑125 (MQ=255)
                                    gAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGC‑GAGGGGGGGGGACTTGAACCCCCa                                                                                                                <  1:1369569/125‑1 (MQ=255)
                                    gAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGC‑GAGGGGGGGGGACTTGAACCCCCACGTCCGTAAGGaca                                                                                                  >  1:399502/1‑139 (MQ=255)
                                      aCCCCCACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCAAGTGCGAGCAATATCAACGTGGTTTTTGGTGC‑GAGGGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACt                                                                                                <  1:1043206/139‑1 (MQ=255)
                                                     aGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGC‑GAGGGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAg                                                                                 <  1:1132787/139‑1 (MQ=255)
                                                        acacTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGC‑GAGGGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAgcgc                                                                              >  1:681621/1‑139 (MQ=255)
                                                        acacCAACACCTGAAGCTAGAATGTGAACCAATTCTGAAACCTCAGGCCAGTACCAACAATGGCAACATGGTTTTTGGTGCGGG‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAgcgc                                                                              <  2:1085303/139‑1 (MQ=9)
                                                                acCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGC‑GAGGGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCa                                                                      <  1:1219985/139‑1 (MQ=255)
                                                                       gCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGGGGTTTTTGGTGC‑GAGGGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGc                                                               <  2:681621/139‑1 (MQ=255)
                                                                         tAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGC‑GAGGGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCa                                                             >  2:1381349/1‑139 (MQ=255)
                                                                          aGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGC‑GAGGGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCAc                                                            >  2:1205725/1‑139 (MQ=255)
                                                                            cgcgTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGC‑GAGGGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCt                                                          >  1:310338/1‑139 (MQ=255)
                                                                                  tACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGC‑GAGGGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCAt                                                    <  2:1322828/139‑1 (MQ=255)
                                                                                  tACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGC‑GAGGGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCAt                                                    <  1:1205725/139‑1 (MQ=255)
                                                                                       aTTCCGCCACGTCCGCCCAGTGCGAGCAAAATCAACGGGGTTTTTTGGGC‑GAGGGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCAt                                               <  2:1484784/139‑1 (MQ=18)
                                                                                         tCCGCCCCCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGC‑GA‑gggggg                                                                                                                               <  2:1481345/56‑1 (MQ=255)
                                                                                         tCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGC‑GAGGGGGGGGGACTTGAAccccc                                                                                                                 <  2:973508/71‑1 (MQ=255)
                                                                                         tCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGC‑GAGGGGGGGGGACTTGAAccccc                                                                                                                 >  1:973508/1‑71 (MQ=255)
                                                                                         tCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGC‑GA‑gggggg                                                                                                                               >  1:1481345/1‑56 (MQ=255)
                                                                                           cGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGC‑GAGGGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGt                                                                            <  2:51114/106‑1 (MQ=255)
                                                                                           cGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGC‑GAGGGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGt                                                                            >  1:51114/1‑106 (MQ=255)
                                                                                            gCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGC‑GAGGGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAAtt                                          >  2:1315492/1‑139 (MQ=255)
                                                                                             ccACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGC‑GAGGGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCAc                                                            <  2:708934/120‑1 (MQ=255)
                                                                                             ccACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGC‑GAGGGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAAAACCTGAAGCTAGCGCTTCTACCAATTCCGCCAc                                                            >  1:708934/1‑120 (MQ=21)
                                                                                                           tGCGAGCAATATCAACGTGGTTTTTGGTGC‑GAGGGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGc                           >  2:775301/1‑139 (MQ=255)
                                                                                                           tGCGAGCAATATCAACGTGGTTTTTGGTGC‑GA‑gggg                                                                                                                                 >  1:793828/1‑36 (MQ=255)
                                                                                                           tGCGAGCAATATCAACGTGGTTTTTGGTGC‑GA‑gggg                                                                                                                                 <  2:793828/36‑1 (MQ=255)
                                                                                                              gAGCAATATCAACGTGGTTTTTGGTGC‑GAGGGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTAc                        >  2:761378/1‑139 (MQ=255)
                                                                                                               aGCAATATCAACGTGGTTTTTGGTGC‑GAGGGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTAcc                       >  1:507844/1‑139 (MQ=255)
                                                                                                                   atatCAACGTGGTTTTTGGTGC‑GAGGGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACgg                   <  1:775301/139‑1 (MQ=255)
                                                                                                                     atCAACGTGGTTTTTGGTGC‑GAGGGGGGGGGACTTGAACCCCCa                                                                                                                >  1:1082822/1‑44 (MQ=18)
                                                                                                                     atCAACGTGGTTTTTGGTGC‑GAGGGGGGGGGACTTGAACCCCCa                                                                                                                <  2:1082822/44‑1 (MQ=18)
                                                                                                                     atCAACGTGGTTTTTGGTGC‑GAGGGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAg                 >  1:1219776/1‑139 (MQ=255)
                                                                                                                     atCAACGTGGTTTTTGGTGC‑GAGGGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAg                 <  1:1040750/139‑1 (MQ=255)
                                                                                                                         aCGTGGTTTTTGGTGC‑GAGGGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGgcg              <  2:1244849/138‑1 (MQ=255)
                                                                                                                         aCGTGGTTTTTGGTGC‑GAGGGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGgcg              >  1:1244849/1‑138 (MQ=255)
                                                                                                                            tGGTTTTTGGTGC‑GAGGGGGGGGGACTTGAACCCCCACGTCCGTa                                                                                                        >  2:439216/1‑45 (MQ=14)
                                                                                                                            tGGTTTTTGGTGC‑GAGGGGGGGGGACTTGAACCCCCACGTCCGTa                                                                                                        <  1:439216/45‑1 (MQ=14)
                                                                                                                              gTTTTTGGTGC‑GAGGGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCt        >  2:751311/1‑139 (MQ=255)
                                                                                                                              gTTTTTGGTGC‑GAGGGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCt        >  2:1200219/1‑139 (MQ=255)
                                                                                                                                ttttGGTGC‑GAGGGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAg      <  1:751311/139‑1 (MQ=255)
                                                                                                                                 tttGGTGC‑GA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCa                                                             >  2:723246/1‑82 (MQ=31)
                                                                                                                                 tttGGTGC‑GA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCa                                                             <  1:723246/82‑1 (MQ=31)
                                                                                                                                    ggTGC‑GAGGGGGGGGGACTTGAACCCCCACGTCCGTAAGGTCACTAACAACTGAAGCTAACGCGTCTACCAATGCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCAGTCCAGTgga  >  2:181707/1‑138 (MQ=21)
                                                                                                                                    ggTGC‑GAGGGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAg                 >  2:1185897/1‑124 (MQ=255)
                                                                                                                                    ggTGC‑GAGGGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAg                 <  1:1185897/124‑1 (MQ=255)
                                                                                                                                            |                                                                                                                                   
TTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGC‑GA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGT  >  NC_000913/4606184‑4606453

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A