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 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 775,571 T→A 50.0% D398E (GAT→GAA)  icd → isocitrate dehydrogenase, specific for NADP+

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE775,5710TA50.0% ‑6.4 / 164.9 128D398E (GAT→GAA) icdisocitrate dehydrogenase, specific for NADP+
Reads supporting (aligned to +/- strand):  ref base T (28/36);  new base A (44/20);  total (72/56)
Fisher's exact test for biased strand distribution p-value = 7.27e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.77e-01

Only 100 of 138 total aligned reads displayed.

GGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGT  >  minE/775512‑775634
                                                           |                                                               
ggTATGGAAGGCGCAATCAACGCGAAAACTGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                                                        >  1:2001127/1‑69 (MQ=255)
ggTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                                                        >  1:293677/1‑69 (MQ=255)
ggTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                                                        >  1:103650/1‑69 (MQ=255)
ggTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                                                        >  1:2089885/1‑69 (MQ=255)
ggTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                                                        >  1:342781/1‑69 (MQ=255)
ggTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaa                                                         <  1:1002253/68‑1 (MQ=255)
ggTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaa                                                         <  1:1600196/68‑1 (MQ=255)
ggTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaa                                                         <  1:215109/68‑1 (MQ=255)
ggTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaa                                                         <  1:413514/68‑1 (MQ=255)
ggTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaa                                                         <  1:66876/68‑1 (MQ=255)
      gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                                                        >  1:2552578/1‑63 (MQ=255)
           cgcAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATg                                             >  1:2528833/1‑69 (MQ=255)
           cgcAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATg                                             >  1:1975014/1‑69 (MQ=255)
            gcAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATg                                             >  1:2859510/1‑68 (MQ=255)
                tCAACGCGAAGACCGTAACCTATGACTTCGAACTTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag                                        >  1:817912/1‑69 (MQ=255)
                tCAACGCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag                                        >  1:2681697/1‑69 (MQ=255)
                tCAACGCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag                                        >  1:2786476/1‑69 (MQ=255)
                tCAACGCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag                                        >  1:2885405/1‑69 (MQ=255)
                tCAACGCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag                                        >  1:1856523/1‑69 (MQ=255)
                tCAACGCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag                                        >  1:293957/1‑69 (MQ=255)
                tCAACGCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag                                        >  1:3222826/1‑69 (MQ=255)
                tCAACGCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag                                        >  1:617799/1‑69 (MQ=255)
                tCAACGCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag                                        >  1:2482237/1‑69 (MQ=255)
                tCAACGCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag                                        >  1:1431610/1‑69 (MQ=255)
                tCAACGCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCag                                        >  1:1428818/1‑69 (MQ=255)
                tCAACCCGAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTa                                                          >  1:418862/1‑51 (MQ=255)
                 cAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCaga                                       >  1:663349/1‑69 (MQ=255)
                  aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAATGCGCTAAGCTGCTGAAATGTTCagag                                      <  1:678165/66‑1 (MQ=255)
                  aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag                                      <  1:2021907/66‑1 (MQ=255)
                  aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag                                      <  1:2662660/66‑1 (MQ=255)
                  aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag                                      <  1:1945265/66‑1 (MQ=255)
                  aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag                                      <  1:2333005/66‑1 (MQ=255)
                  aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag                                      <  1:2167968/66‑1 (MQ=255)
                  aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag                                      <  1:307168/66‑1 (MQ=255)
                  aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag                                      <  1:328662/66‑1 (MQ=255)
                  aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag                                      <  1:3299891/66‑1 (MQ=255)
                  aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag                                      <  1:3386772/66‑1 (MQ=255)
                  aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag                                      <  1:412918/66‑1 (MQ=255)
                  aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag                                      <  1:1222316/66‑1 (MQ=255)
                  aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag                                      <  1:61971/66‑1 (MQ=255)
                  aatgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag                                      <  1:1134059/66‑1 (MQ=255)
                  aaCGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCagag                                      >  1:1719292/1‑69 (MQ=255)
                  aaCGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCagag                                      >  1:1683526/1‑69 (MQ=255)
                  aaCGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCagag                                      >  1:3304954/1‑69 (MQ=255)
                  aaCGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCagag                                      >  1:48945/1‑69 (MQ=255)
                   atgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag                                      <  1:2992589/66‑1 (MQ=255)
                    cgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTaa                                                         >  1:715857/1‑48 (MQ=38)
                    cgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAAGTGCTGAAATGTTCAGAGtt                                    >  1:1091785/1‑69 (MQ=255)
                    cgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCAGAGtt                                    >  1:2330927/1‑69 (MQ=255)
                    cgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCAGAGtt                                    >  1:458608/1‑69 (MQ=255)
                    cgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCAGAGtt                                    >  1:1572673/1‑69 (MQ=255)
                    cgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCAGAGtt                                    >  1:2806041/1‑69 (MQ=255)
                    cgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCAGAGtt                                    >  1:1165290/1‑69 (MQ=255)
                    cgcgAAGACCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAACTGCTGAAATGTTCAGAGtt                                    >  1:2202576/1‑69 (MQ=255)
                        aagaCCGTAACCTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCagag                                      <  1:16376/60‑1 (MQ=255)
                        aaaaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGt                                <  1:1287802/69‑1 (MQ=255)
                        aaaaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGt                                <  1:462317/69‑1 (MQ=255)
                        aaaaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGt                                <  1:2858904/69‑1 (MQ=255)
                        aaaaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGt                                <  1:1934197/69‑1 (MQ=255)
                         aaaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGt                                <  1:2671653/68‑1 (MQ=255)
                              gTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGAcgcg                          <  1:1309409/69‑1 (MQ=255)
                                          ttCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaaaa               <  1:152698/68‑1 (MQ=255)
                                          ttCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaaaa               <  1:1072836/68‑1 (MQ=255)
                                          ttCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaaaa               <  1:761351/68‑1 (MQ=255)
                                            cGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACa             >  1:1368037/1‑68 (MQ=255)
                                            cGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACa             >  1:2135354/1‑68 (MQ=255)
                                            cGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACa             >  1:1818368/1‑68 (MQ=255)
                                            cGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACa             >  1:3204883/1‑68 (MQ=255)
                                            cGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATAGAAAACa             >  1:586691/1‑68 (MQ=255)
                                              aGCGTCTGATGGATGGCGCTAAACT‑CTGAAATCTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt          <  1:2737585/68‑1 (MQ=255)
                                               gCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt          <  1:1666042/68‑1 (MQ=255)
                                               gCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt          <  1:2064121/68‑1 (MQ=255)
                                               gCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt          <  1:1755709/68‑1 (MQ=255)
                                               gCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt          <  1:3096993/68‑1 (MQ=255)
                                               gCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt          <  1:1892782/68‑1 (MQ=255)
                                               gCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt          <  1:2888772/68‑1 (MQ=255)
                                               gCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt          <  1:1903743/68‑1 (MQ=255)
                                               gCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt          <  1:965042/68‑1 (MQ=255)
                                               gCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt          <  1:1196288/68‑1 (MQ=255)
                                                    tGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGATGCGATCATCAAGAATATGTAAtcac    >  1:755905/1‑66 (MQ=255)
                                                    tGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGATGCGATCATCAAGAATATGTAAtcac    >  1:52905/1‑66 (MQ=255)
                                                    tGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGATGCGATCATCAAGAATATGTAAtcac    >  1:1776108/1‑66 (MQ=255)
                                                    tGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGATGCGATCATCAAGAATATGTAAtcac    >  1:1303656/1‑66 (MQ=255)
                                                    tGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGATGCGATCATCAAGAATATGTAAtcac    >  1:1504964/1‑66 (MQ=255)
                                                    tGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGATGCGATCATCAAGAATATGTAAtcac    >  1:1780087/1‑66 (MQ=255)
                                                    tGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGATGCGATCATCAAGAATATGTAAtcac    >  1:282178/1‑66 (MQ=255)
                                                    tGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGATGCGATCATCAAGAATATGTAAtcac    >  1:2734080/1‑66 (MQ=255)
                                                    tGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGATGCGATCATCAAGAATATGTAAtcac    >  1:2697353/1‑66 (MQ=255)
                                                    tGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGATGCGATCATCAAGAATATGTAAtcac    >  1:2073004/1‑66 (MQ=255)
                                                    tGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGATGCGATCATCAAGAATATGTAAtcac    >  1:2495474/1‑66 (MQ=255)
                                                    tGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGATGCGATCATCAAGAATATGTAAtca     >  1:1910976/1‑66 (MQ=255)
                                                    tGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGATTggag                               >  1:2853218/1‑40 (MQ=25)
                                                      atggatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGt  >  1:804584/1‑69 (MQ=255)
                                                      atggatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGt  >  1:98499/1‑69 (MQ=255)
                                                      atggatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGt  >  1:506864/1‑69 (MQ=255)
                                                      atggatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGt  >  1:2938651/1‑69 (MQ=255)
                                                      atggatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGt  >  1:2424204/1‑69 (MQ=255)
                                                      atggatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGt  >  1:2205448/1‑69 (MQ=255)
                                                      atggatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGt  >  1:1265009/1‑69 (MQ=255)
                                                      atggatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGt  >  1:1032596/1‑69 (MQ=255)
                                                           |                                                               
GGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGT  >  minE/775512‑775634

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A