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 2,562,263 T→C 44.0% A53A (GCA→GCG)  lldR ← DNA‑binding transcriptional repressor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,562,2630TC44.0% 24.5 / 80.3 100A53A (GCA→GCG) lldRDNA‑binding transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base T (18/38);  new base C (29/15);  total (47/53)
Fisher's exact test for biased strand distribution p-value = 1.16e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 114 total aligned reads displayed.

ACGCCAGCGAATAAACGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTGCATCGCCAGTTGGCGCTCAGCG  >  minE/2562200‑2562326
                                                               |                                                               
aCGCCAGCGAATAAACGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAg                                                            >  1:3135761/1‑69 (MQ=255)
aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCa                                                             >  1:436689/1‑68 (MQ=255)
aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCa                                                             >  1:2210985/1‑68 (MQ=255)
aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAg                                                            >  1:967578/1‑69 (MQ=255)
aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAg                                                            >  1:1592134/1‑69 (MQ=255)
aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAg                                                            >  1:2815374/1‑69 (MQ=255)
aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAg                                                            >  1:3236630/1‑69 (MQ=255)
aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAg                                                            >  1:278270/1‑69 (MQ=255)
aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAg                                                            >  1:1109741/1‑69 (MQ=255)
aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAg                                                            >  1:514834/1‑69 (MQ=255)
aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAg                                                            >  1:1869038/1‑69 (MQ=255)
aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAg                                                            >  1:1958370/1‑69 (MQ=255)
aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAg                                                            >  1:802202/1‑69 (MQ=255)
aCGCCAGCGAATAAACGTCCCGCCGCCAAGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAg                                                            >  1:395311/1‑69 (MQ=255)
       cGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAGCGCCTcg                                                     >  1:17662/1‑69 (MQ=255)
       cGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAGCGCCTcg                                                     >  1:2362737/1‑69 (MQ=255)
       cGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAGCGCCTcg                                                     >  1:2536618/1‑69 (MQ=255)
       cGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAGCGCCTcg                                                     >  1:1931601/1‑69 (MQ=255)
       cGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAGCGCCTcg                                                     >  1:1591865/1‑69 (MQ=255)
       cGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAGCGCCTcg                                                     >  1:1345581/1‑69 (MQ=255)
       cGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAGCGCCTcg                                                     >  1:3342586/1‑69 (MQ=255)
       cGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAGCGCCTcg                                                     >  1:1211911/1‑69 (MQ=255)
       cGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAGCGCCTcg                                                     >  1:480546/1‑69 (MQ=255)
       cGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAGCGCCTcg                                                     >  1:1114674/1‑69 (MQ=255)
       cGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAGCGCCTcg                                                     >  1:56595/1‑69 (MQ=255)
       cGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAGCGCCTcg                                                     >  1:662973/1‑69 (MQ=255)
             aaCGTCCCGCCGCCGCGTCGACTGATCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAg                                                >  1:1012729/1‑68 (MQ=255)
             aaCGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAg                                                >  1:1640195/1‑68 (MQ=255)
             aaCGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAg                                                >  1:1879949/1‑68 (MQ=255)
             aaCGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAg                                                >  1:784326/1‑68 (MQ=255)
             aaCGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAg                                                >  1:1873545/1‑68 (MQ=255)
             aaCGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAg                                                >  1:477900/1‑68 (MQ=255)
               cGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTg                                              <  1:3383000/68‑1 (MQ=255)
               cGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTg                                              <  1:1603699/68‑1 (MQ=255)
               cGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTg                                              <  1:2902873/68‑1 (MQ=255)
               cGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTg                                              <  1:3181433/68‑1 (MQ=255)
               cGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTg                                              <  1:3213057/68‑1 (MQ=255)
               cGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTg                                              <  1:322245/68‑1 (MQ=255)
               cGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTg                                              <  1:2194821/68‑1 (MQ=255)
               cGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTg                                              <  1:3235681/68‑1 (MQ=255)
               cGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTg                                              <  1:3350025/68‑1 (MQ=255)
               cGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTg                                              <  1:756462/68‑1 (MQ=255)
               cGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTg                                              <  1:1936547/68‑1 (MQ=255)
               cGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTg                                              <  1:852750/68‑1 (MQ=255)
                     gccgccgcGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACg                                       <  1:1897085/69‑1 (MQ=255)
                     gccgccgcGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACg                                       <  1:401970/69‑1 (MQ=255)
                     gccgccgcGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACg                                       <  1:837777/69‑1 (MQ=255)
                     gccgccgcGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACg                                       <  1:248944/69‑1 (MQ=255)
                        gccgcGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGa                                    <  1:1005308/69‑1 (MQ=255)
                        gccgcGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGa                                    <  1:494467/69‑1 (MQ=255)
                        gccgcGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGa                                    <  1:1600278/69‑1 (MQ=255)
                              tCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTg                                              <  1:1935041/53‑1 (MQ=255)
                                   tGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGt                          >  1:358390/1‑68 (MQ=255)
                                   tGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGt                          >  1:898074/1‑68 (MQ=255)
                                   tGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGt                          >  1:257678/1‑68 (MQ=255)
                                           aCGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTTCGTGATACGCCGAGTTGCATCGcc                 <  1:605982/69‑1 (MQ=255)
                                           aCGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTGCATCGcc                 <  1:445156/69‑1 (MQ=255)
                                           aCGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTGCATCGcc                 <  1:2588515/69‑1 (MQ=255)
                                           aCGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTGCATCGcc                 <  1:1982562/69‑1 (MQ=255)
                                           aCGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTGCATCGcc                 <  1:1048227/69‑1 (MQ=255)
                                           aCGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTGCATCGcc                 <  1:530981/69‑1 (MQ=255)
                                           aCGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTGCATCGcc                 <  1:469965/69‑1 (MQ=255)
                                           aCGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTGCATCGcc                 <  1:449362/69‑1 (MQ=255)
                                           aCGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTGCATCGcc                 <  1:2818188/69‑1 (MQ=255)
                                           aCGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTGCATCGcc                 <  1:1268446/69‑1 (MQ=255)
                                           aCGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTGCATCGcc                 <  1:2176598/69‑1 (MQ=255)
                                           aCGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTGCATCGcc                 <  1:2910078/69‑1 (MQ=255)
                                            cGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTGCATCGCCa                >  1:1896919/1‑69 (MQ=255)
                                            cGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTGCATCGCCa                >  1:1039537/1‑69 (MQ=255)
                                            cGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTGCATCGCCa                >  1:1930493/1‑69 (MQ=255)
                                                      tacCAGTTTCGCCTGCGCCTCGCGCAGTGAATTTCTCGACACGCCGa                            <  1:2431177/46‑1 (MQ=255)
                                                      tacCAGTTTCGCCAGCGCCTCGCGCAGTGAATTTCTCGACACGCCGa                            <  1:1033080/46‑1 (MQ=21)
                                                      tacCAGTTTCGCCAGCGCCTCGCGCAGTGAATTTCTCGACACGCCGa                            <  1:3112986/46‑1 (MQ=21)
                                                      tacCAGTTTCGCCAGCGCCTCGCGCAGTGAATTTCTCGACACGCCGa                            <  1:1090280/46‑1 (MQ=21)
                                                      tacCAGTTTCGCCAGCGCCTCGCGCAGTGAATTTCTCGACACGCCGa                            <  1:2700641/46‑1 (MQ=21)
                                                      tacCAGTTTCGCCAGCGCCTCGCGCAGTGAATTTCTCGACACGCCGa                            <  1:1167155/46‑1 (MQ=21)
                                                      tacCAGTTTCGCCAGCGCCTCGCGCAGTGAATTTCTCGACACGCCGa                            <  1:2009729/46‑1 (MQ=21)
                                                      tacCAGTTTCGCCAGCGCCTCGCGCAGTGAATTTCTCGACACGCCGa                            <  1:3146482/46‑1 (MQ=21)
                                                      tacCAGTTTCGCCAGCGCCTCGCGCAGTGAATTTCTCGACACGCCGa                            <  1:2058380/46‑1 (MQ=21)
                                                      tacCAGTTTCGCCAGCGCCTCGCGCAGTGAATTTCTCGACACGCCGa                            <  1:1301985/46‑1 (MQ=21)
                                                      tacCAGTTTCGCCAGCGCCTCGCGCAGTGAATTTCTCGACACGCCGa                            <  1:2712408/46‑1 (MQ=21)
                                                      tacCAGTTTCGCCAGCGCCTCGCGCAGTGAATTTCTCGACACGCCGa                            <  1:964275/46‑1 (MQ=21)
                                                      tacCAGTTTCGCCAGCGCCTCGCGCAGTGAATTTCTCGACACGCCGa                            <  1:2125345/46‑1 (MQ=21)
                                                      tacCAGTTTCGCCAGCGCCTCGCGCAGTGAATTTCTCGACACGCCGa                            <  1:1318233/46‑1 (MQ=21)
                                                      cacCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTGCATCGCCAGTTGGCGCTc      >  1:742118/1‑69 (MQ=255)
                                                      cacCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTGCATCGCCAGTTGGCGCTc      >  1:3259958/1‑69 (MQ=255)
                                                           gTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTGCATCGCCAGTTGGCGCTCAGCg  >  1:884984/1‑68 (MQ=255)
                                                           gTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTGCATCGCCAGTTGGCGCTCAGCg  >  1:3290094/1‑68 (MQ=255)
                                                              ttGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTg                        >  1:861742/1‑43 (MQ=255)
                                                              ttGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTg                        >  1:2504435/1‑43 (MQ=255)
                                                              ttGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTg                        <  1:2599692/43‑1 (MQ=255)
                                                              ttGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTg                        <  1:1757315/43‑1 (MQ=255)
                                                              ttGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTg                        <  1:2678508/43‑1 (MQ=255)
                                                              ttGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTg                        <  1:731106/43‑1 (MQ=255)
                                                              ttGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTg                        >  1:3070647/1‑43 (MQ=255)
                                                              ttGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTg                        <  1:3104996/43‑1 (MQ=255)
                                                              ttGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTg                        <  1:1545705/43‑1 (MQ=255)
                                                              ttGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTg                        >  1:166714/1‑43 (MQ=255)
                                                              ttGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTg                        >  1:2063129/1‑43 (MQ=255)
                                                              ttGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTg                        <  1:1347597/43‑1 (MQ=255)
                                                               |                                                               
ACGCCAGCGAATAAACGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGATACGCCGAGTTGCATCGCCAGTTGGCGCTCAGCG  >  minE/2562200‑2562326

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