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 1,938,253 A→G 44.1% H253H (CAT→CAC)  xerD ← site‑specific tyrosine recombinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,938,2530AG44.1% 19.5 / 75.0 93H253H (CAT→CAC) xerDsite‑specific tyrosine recombinase
Reads supporting (aligned to +/- strand):  ref base A (25/27);  new base G (14/27);  total (39/54)
Fisher's exact test for biased strand distribution p-value = 2.08e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01

Only 100 of 111 total aligned reads displayed.

TGGTGGAGAGATCGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAACACATGCGGTGACAGCTTTTCGCTGTCGATACCCGCCAGCACAG  >  minE/1938186‑1938320
                                                                   |                                                                   
tggtggAGAGATCGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCACCATGATTTAATAAAt                                                                    <  1:108278/69‑1 (MQ=255)
tggtggAGAGATCGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCACCATGATTTAATAAAt                                                                    <  1:3229210/69‑1 (MQ=255)
tggtggAGAGATCGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCACCATGATTTAATAAAt                                                                    <  1:1852875/69‑1 (MQ=255)
 ggtggAGAGATCGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCACCATGATTTAATAAATg                                                                   <  1:357488/69‑1 (MQ=255)
            cGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAg                                                        >  1:428605/1‑69 (MQ=255)
            cGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAg                                                        >  1:283882/1‑69 (MQ=255)
            cGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAg                                                        >  1:3431638/1‑69 (MQ=255)
                     ccAGTAGCATCTGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACTCa                                               <  1:502807/69‑1 (MQ=255)
                     ccAGTAGCATCTGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCa                                               <  1:82827/69‑1 (MQ=255)
                     ccAGTAGCATCTGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCa                                               <  1:1222736/69‑1 (MQ=255)
                     ccAGTAGCATCTGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCa                                               <  1:1140483/69‑1 (MQ=255)
                     ccAGTAGCATCTGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCa                                               <  1:3383325/69‑1 (MQ=255)
                     ccAGTAGCATCTGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCa                                               <  1:1940934/69‑1 (MQ=255)
                     ccAGTAGCATCTGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCa                                               <  1:3339364/69‑1 (MQ=255)
                     ccAGTAGCATCTGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCa                                               <  1:3314084/69‑1 (MQ=255)
                     ccAGTAGCATCTGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCa                                               <  1:2032157/69‑1 (MQ=255)
                     ccAGTAGCATCTGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCa                                               <  1:1792729/69‑1 (MQ=255)
                     ccAGTAGCATCTGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCa                                               <  1:2997469/69‑1 (MQ=255)
                     ccAGTAGCATCTGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCa                                               <  1:2184208/69‑1 (MQ=255)
                     ccAGTAGCATCTGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCa                                               <  1:2992552/69‑1 (MQ=255)
                     ccAGTAGCATCTGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCa                                               <  1:295012/69‑1 (MQ=255)
                     ccAGTAGCATCTGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCa                                               <  1:2462475/69‑1 (MQ=255)
                     ccAGTAGCATCTGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCa                                               <  1:2863038/69‑1 (MQ=255)
                     ccAGTAGCATCTGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCa                                               <  1:862896/69‑1 (MQ=255)
                     ccAGTAGCATCTGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCa                                               <  1:797978/69‑1 (MQ=255)
                     ccAGTAGCATCTGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCa                                               <  1:1704433/69‑1 (MQ=255)
                     ccAGTAGCATCTGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCa                                               <  1:1347524/69‑1 (MQ=255)
                     ccAGTAGCATCTGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCa                                               <  1:1653190/69‑1 (MQ=255)
                     ccAGTAGCATCTGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCa                                               <  1:1353057/69‑1 (MQ=255)
                     ccAGTAGCATCTGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCa                                               <  1:599293/69‑1 (MQ=255)
                     ccAGTAGCATCTGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCa                                               <  1:1498877/69‑1 (MQ=255)
                     ccAGTAGCATCTGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCa                                               <  1:1422129/69‑1 (MQ=255)
                        gTAGCATCTGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAaca                                            <  1:1971454/69‑1 (MQ=255)
                        gTAGCATCTGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAaca                                            <  1:1990500/69‑1 (MQ=255)
                           gCATCTGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAACACAt                                         >  1:1703390/1‑69 (MQ=255)
                           gCATCTGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAACACAt                                         >  1:1646881/1‑69 (MQ=255)
                                tGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGa                                                   >  1:523821/1‑54 (MQ=255)
                                tGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGa                                                   >  1:1239542/1‑54 (MQ=255)
                                tGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGa                                                   >  1:2383447/1‑54 (MQ=255)
                                tGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGa                                                   >  1:3223931/1‑54 (MQ=255)
                                tGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGa                                                   >  1:465949/1‑54 (MQ=255)
                                tGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGa                                                   >  1:435877/1‑54 (MQ=255)
                                tGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGa                                                   >  1:1753262/1‑54 (MQ=255)
                                tGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGa                                                   >  1:807148/1‑54 (MQ=255)
                                tGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAaca                                            <  1:3138009/61‑1 (MQ=255)
                                tGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAaca                                            >  1:1059824/1‑61 (MQ=255)
                                tGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAaca                                            <  1:666335/61‑1 (MQ=255)
                                tGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAaca                                            <  1:808725/61‑1 (MQ=255)
                                tGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAaca                                            >  1:102379/1‑61 (MQ=255)
                                tGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAaca                                            >  1:1691544/1‑61 (MQ=255)
                                tGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAaca                                            <  1:1991035/61‑1 (MQ=255)
                                tGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAaca                                            >  1:1360913/1‑61 (MQ=255)
                                tGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAaca                                            <  1:2063796/61‑1 (MQ=255)
                                tGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAaca                                            <  1:2112318/61‑1 (MQ=255)
                                tGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAaca                                            >  1:2246609/1‑61 (MQ=255)
                                tGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAaca                                            <  1:1176957/61‑1 (MQ=255)
                                tGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTAGCAAAAGCGTGa                                                   >  1:1157842/1‑54 (MQ=255)
                                tGCACCACGCGTAAATCCGCACCATGATTTAATAAAAGAGTGGCAAAAg                                                        >  1:1127597/1‑49 (MQ=255)
                                tGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAg                                                                 >  1:328414/1‑40 (MQ=38)
                                tGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCAACACATGCGGt                                    >  1:476440/1‑69 (MQ=255)
                                tGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCAACACATGCGGt                                    >  1:1861574/1‑69 (MQ=255)
                                tGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCAACACATGCGGt                                    >  1:588904/1‑69 (MQ=255)
                                tGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCAACACATGCGGt                                    >  1:2787190/1‑69 (MQ=255)
                                tGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCAACACATGCGGt                                    >  1:3335642/1‑69 (MQ=255)
                                tGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCAACACATGCGGt                                    >  1:669749/1‑69 (MQ=255)
                                tGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCAACACATGCGGt                                    >  1:3267203/1‑69 (MQ=255)
                                tGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCAACACATGCGGt                                    >  1:449692/1‑69 (MQ=255)
                                tGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCAACACATGCGGt                                    >  1:3171997/1‑69 (MQ=255)
                                tGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCAACACATGCGGt                                    >  1:690640/1‑69 (MQ=255)
                                tGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCAACACATGCGGt                                    >  1:3026316/1‑69 (MQ=255)
                                tGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCAACACATGCGGt                                    >  1:2116239/1‑69 (MQ=255)
                                tGCACCACGCGCAAATCCGCACCATGATTTAATAAGTGAGTGGCAAAAGCGTGACGCAACACATGCGGt                                    >  1:292392/1‑69 (MQ=255)
                                tGCACAACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAaca                                            <  1:2956824/61‑1 (MQ=255)
                                    ccacGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAACACATGCGGt                                    <  1:1711552/65‑1 (MQ=255)
                                    ccacGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAACACATGCGGt                                    <  1:747935/65‑1 (MQ=255)
                                    ccacGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAACACATGCGGt                                    <  1:835580/65‑1 (MQ=255)
                                    ccacGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAACACATGCGGt                                    <  1:3193060/65‑1 (MQ=255)
                                          gTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTCACGCAaca                                            <  1:2644274/51‑1 (MQ=255)
                                                 cGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAACACATGCGGTGACAGCTTTTCGCTGTc                   <  1:2821440/69‑1 (MQ=255)
                                                 cGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAACACATGCGGTGACAGCTTTTCGCTGTc                   <  1:1517854/69‑1 (MQ=255)
                                                 cGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAACACATGCGGTGACAGCTTTTCGCTGTc                   <  1:2013395/69‑1 (MQ=255)
                                                   cACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAACACATGCGGTGACAGCTTTTCTCTGTCGa                 <  1:1369256/69‑1 (MQ=255)
                                                   cACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAACACATGCGGTGACAGCTTTTCGCTGTCGa                 <  1:225426/69‑1 (MQ=255)
                                                      cATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAACACATGCGGTGACAGCTTTTCGCTGTc                   <  1:2773158/64‑1 (MQ=255)
                                                                  aaTGAGTGGCAAAAGCGTGACGCAACACATGCGGTGACAGCTTTTCGCTGTCGATAccc            <  1:1522449/59‑1 (MQ=255)
                                                                  aaTGAGTGGCAAAAGCGTGACGCAACACATGCGGTGACAGCTTTTCGCTGTCGATAccc            <  1:2575756/59‑1 (MQ=255)
                                                                  aaTGAGTGGCAAAAGCGTGACGCAACACATGCGGTGACAGCTTTTCGCTGTCGATAccc            <  1:79884/59‑1 (MQ=255)
                                                                  aaTGAGTGGCAAAAGCGTGACGCAACACATGCGGTGACAGCTTTTCGCTGTCGATACCCGCcagcacag  >  1:2639401/1‑69 (MQ=255)
                                                                  aaTGAGTGGCAAAAGCGTGACGCAACACATGCGGTGACAGCTTTTCGCTGTCGATACCCGCcagcacag  >  1:429383/1‑69 (MQ=255)
                                                                  aaTGAGTGGCAAAAGCGTGACGCAACACATGCGGTGACAGCTTTTCGCTGTCGATACCCGCcagcacag  >  1:818311/1‑69 (MQ=255)
                                                                  aaTGAGTGGCAAAAGCGTGACGCAACACATGCGGTGACAGCTTTTCGCTGTCGATACCCGCcagcacag  >  1:1227918/1‑69 (MQ=255)
                                                                  aaTGAGTGGCAAAAGCGTGACGCAACACATGCGGTGACAGCTTTTCGCTGTCGATACCCGCcagcacag  >  1:796313/1‑69 (MQ=255)
                                                                  aaTGAGTGGCAAAAGCGTGACGCAACACATGCGGTGACAGCTTTTCGCTGTCGATACCCGCcagcacag  >  1:750943/1‑69 (MQ=255)
                                                                  aaTGAGTGGCAAAAGCGTGACGCAACACATGCGGTGACAGCTTTTCGCTGTCGATACCCGCcagcacag  >  1:2112966/1‑69 (MQ=255)
                                                                  aaTGAGTGGCAAAAGCGTGACGCAACACATGCGGTGACAGCTTTTCGCTGTCGATACCCGCcagcacag  >  1:3336806/1‑69 (MQ=255)
                                                                  aaTGAGTGGCAAAAGCGTGACGCAACACATGCGGTGACAGCTTTTCGCTGTCGATACCCGCcagcacag  >  1:1900376/1‑69 (MQ=255)
                                                                  aaTGAGTGGCAAAAGCGTGACGCAACACATGCGGTGACAGCTTTTCGCTGTCGATACCCGCcagcacag  >  1:1746580/1‑69 (MQ=255)
                                                                  aaTGAGTGGCAAAAGCGTGACGCAACACATGCGGTGACAGCTTTTCGCTGTCGATACCCGCcagcacag  >  1:469028/1‑69 (MQ=255)
                                                                  aaTGAGTGGCAAAAGCGTGACGCAACACATGCGGTGACAGCTTTTCGCTGTCGATACCCGCcagcaca   >  1:1539002/1‑68 (MQ=255)
                                                                   aTGAGTGGCAAAAGCGTGACGCAACACATGCGGTGACAGCTTTTCGCTGTCGATAccc            <  1:2629112/58‑1 (MQ=255)
                                                                   |                                                                   
TGGTGGAGAGATCGCTGTGGCCCAGTAGCATCTGCACCACGCGTAAATCCGCACCATGATTTAATAAATGAGTGGCAAAAGCGTGACGCAACACATGCGGTGACAGCTTTTCGCTGTCGATACCCGCCAGCACAG  >  minE/1938186‑1938320

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