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 2,676,992 C→T 20.9% H247H (CAC→CAT)  bioH → carboxylesterase of pimeloyl‑CoA synthesis

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,676,9920CT20.9% 109.2 / 18.8 76H247H (CAC→CAT) bioHcarboxylesterase of pimeloyl‑CoA synthesis
Reads supporting (aligned to +/- strand):  ref base C (24/36);  new base T (4/12);  total (28/48)
Fisher's exact test for biased strand distribution p-value = 3.84e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.94e-01

AGCGAATCATATATCTTCGCCAAAGCGGCCCATGCGCCATTTATTTCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTGGCTTTTGAAATGGCGAGACAGAACTTTACTG  >  minE/2676924‑2677056
                                                                    |                                                                
aGCGAATCATATATCTTCGCCAAAGCGGCCCATGCGCCATTTATTTCGCATCCGGCCGAGTTTTGTCAc                                                                  >  1:2854819/1‑69 (MQ=255)
aGCGAATCATATATCTTCGCCAAAGCGGCCCATGCGCCATTTATTTCGCATCCGGCCGAGTTTTGTCAc                                                                  >  1:111298/1‑69 (MQ=255)
aGCGAATCATATATCTTCGCCAAAGCGGCCCATGCGCCATTTATTTCGCATCCGGCCGAGTTTTGTCAc                                                                  >  1:171928/1‑69 (MQ=255)
aGCGAATCATATATCTTCGCCAAAGCGGCCCATGCGCCATTTATTTCGCATCCGGCCGAGTTTTGTCAc                                                                  >  1:1293724/1‑69 (MQ=255)
aGCGAATCATATATCTTCGCCAAAGCGGCCCATGCGCCATTTATTTCGCATCCGGCCGAGTTTTGTCAc                                                                  >  1:3069397/1‑69 (MQ=255)
aGCGAATCATATATCTTCGCCAAAGCGGCCCATGCGCCATTTATTTCGCATCCGGCCGAGTTTT‑TCAcc                                                                 >  1:2459099/1‑69 (MQ=255)
 gCGAATCATATATCTTCGCCAAAGCGGCCCATGCGCCATTTATTTCGCATCCGGCCGAGTTTTGTCAcc                                                                 >  1:2633256/1‑69 (MQ=255)
 gCGAATCATATATCTTCGCCAAAGCGGCCCATGCGCCATTTATTTCGCATCCGGCCGAGTTTTGTCAcc                                                                 >  1:150848/1‑69 (MQ=255)
           tatCTTCGCCAAAGCGGCCCATGCGCCATTTATTTCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGc                                                       >  1:1909607/1‑69 (MQ=255)
           tatCTTCGCCAAAGCGGCCCATGCGCCATTTATTTCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGc                                                       >  1:603157/1‑69 (MQ=255)
           tatCTTCGCCAAAGCGGCCCATGCGCCATTTATTTCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGc                                                       >  1:3245858/1‑69 (MQ=255)
           tatCTTCGCCAAAGCGGCCCATGCGCCATTTATTTCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGc                                                       >  1:1591542/1‑69 (MQ=255)
           tatCTTCGCCAAAGCGGCCCATGCGCCATTTATTTCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGc                                                       >  1:2197439/1‑69 (MQ=255)
           tatCTTCGCCAAAGCGGCCCATGCGCCATTTATTTCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGc                                                       >  1:2209787/1‑69 (MQ=255)
           tatCTTCGCCAAAGCGGCCCATGCGCCATTTATTTCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGc                                                       >  1:1309270/1‑69 (MQ=255)
           tatCTTCGCCAAAGCGGCCCATGCGCCATTTATTTCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGc                                                       >  1:1240760/1‑69 (MQ=255)
           tatCTTCGCCAAAGCGGCCCATGCGCCATTTATTTCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGc                                                       >  1:2671951/1‑69 (MQ=255)
           tatCTTCGCCAAAGCGGCCCATGCGCCATTTATTTCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGc                                                       >  1:2724358/1‑69 (MQ=255)
           tatCTTCGCCAAAGCGGCCCATGCGCCATTTATTTCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGc                                                       >  1:27285/1‑69 (MQ=255)
           tatCTTCGCCAAAGCGGCCCATGCGCCATTTATTTCGCATCCGGCCGAGTATTGTCACCTGCTGGTGGc                                                       >  1:243190/1‑69 (MQ=255)
                 cGCCAAAGCGGCCCATGCGCCGTTTATTTCACATCCGGACGAGTTTTGTCATCTGCTGGTGGCGTTGa                                                  >  1:3301770/1‑68 (MQ=255)
                 cGCCAAAGCGGCCCATGCGCCGTTTATTTCACATCCGGACGAGTTTTGTCATCTGCTGGTGGCGTTGa                                                  >  1:1124683/1‑68 (MQ=255)
                 cGCCAAAGCGGCCCATGCGCCGTTTATTTCACATCCGGACGAGTTTTGTCATCTGCTGGTGGCGTTGa                                                  >  1:127340/1‑68 (MQ=255)
                 cGCCAAAGCGGCCCATGCGCCGTTTATTTCACATCCGGACGAGTTTTGTCATCTGCTGGTGGCGTTGa                                                  >  1:1287555/1‑68 (MQ=255)
                    cAAAGCGGCCCATGCGCCATTTATTTCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGCGTTGAAGc                                               <  1:68522/68‑1 (MQ=255)
                    cAAAGCGGCCCATGCGCCATTTATTTCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGCGTTGAAGc                                               <  1:2638208/68‑1 (MQ=255)
                    cAAAGCGGCCCATGCGCCATTTATTTCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGCGTTGAAGc                                               <  1:2595085/68‑1 (MQ=255)
                    cAAAGCGGCCCATGCGCCATTTATTTCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGCGTTGAAGc                                               <  1:244959/68‑1 (MQ=255)
                    cAAAGCGGCCCATGCGCCATTTATTTCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGCGTTGAAGc                                               <  1:2265605/68‑1 (MQ=255)
                    cAAAGCGGCCCATGCGCCATTTATTTCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGCGTTGAAGc                                               <  1:1400880/68‑1 (MQ=255)
                     aaaGCGGCCCATGCGCCATTTATTTCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGCGTTGAAGc                                               <  1:1382861/67‑1 (MQ=255)
                           gCCCATGCGCCATTTATTTCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGCGTTGAAGCAGAGGgtg                                       <  1:2959093/69‑1 (MQ=255)
                           gCCCATGCGCCATTTATTTCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGCGTTGAAGCAGAGGgtg                                       <  1:2972316/69‑1 (MQ=255)
                            cccATGCGCCATTTATTTCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGCGTTGAAGCAGAGGgtgt                                      <  1:504222/69‑1 (MQ=255)
                            cccATGCGCCATTTATTTCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGCGTTGAAGCAGAGGgtgt                                      <  1:2940908/69‑1 (MQ=255)
                            cccATGCGCCATTTATTTCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGCGTTGAAGCAGAGGgtg                                       <  1:2600090/68‑1 (MQ=255)
                             ccATGCGCCATTTATTTCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGCGTTGAAGCAGAGGgtgt                                      <  1:908029/68‑1 (MQ=255)
                                  cgcCATTTATTTCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTgg                                >  1:3049258/1‑69 (MQ=255)
                                  cgcCATTTATTTCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTgg                                >  1:2211661/1‑69 (MQ=255)
                                  cgcCATTTATTTCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTgg                                >  1:1436247/1‑69 (MQ=255)
                                  cgcCATTTATTTCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTgg                                >  1:2915997/1‑69 (MQ=255)
                                  cgcCATTTATTTCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTgg                                >  1:2081866/1‑69 (MQ=255)
                                         tatttCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTGGCTTTTGa                         <  1:1051387/69‑1 (MQ=255)
                                         tatttCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTGGCTTTTGa                         <  1:3083145/69‑1 (MQ=255)
                                         tatttCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTGGCTTTTGa                         >  1:947912/1‑69 (MQ=255)
                                         tatttCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTGGCTTTTGa                         >  1:33401/1‑69 (MQ=255)
                                         tatttCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTGGCTTTTGa                         <  1:3339124/69‑1 (MQ=255)
                                         tatttCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTGGCTTTTGa                         <  1:974259/69‑1 (MQ=255)
                                         tatttCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTGGCTTTTGa                         <  1:817432/69‑1 (MQ=255)
                                         tatttCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTGGCTTTTGa                         <  1:898535/69‑1 (MQ=255)
                                         tatttCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTGGCTTTTGa                         >  1:3044876/1‑69 (MQ=255)
                                         tatttCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTGGCTTTTGa                         >  1:3177297/1‑69 (MQ=255)
                                         tatttCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTGGCTTTTGa                         >  1:2721289/1‑69 (MQ=255)
                                         tatttCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTGGCTTTTGa                         <  1:2785126/69‑1 (MQ=255)
                                         tatttCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTGGCTTTTGa                         >  1:2499903/1‑69 (MQ=255)
                                         tatttCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTGGCTTTTGa                         <  1:2462634/69‑1 (MQ=255)
                                         tatttCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTGGCTTTTGa                         <  1:1166783/69‑1 (MQ=255)
                                         tatttCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTGGCTTTTGa                         <  1:1816715/69‑1 (MQ=255)
                                         tatttCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTGGCTTTTGa                         >  1:2436364/1‑69 (MQ=255)
                                                           gTTTTGTCACCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTGGCTTTTGAAATGGCGAGACAGAACtt       <  1:1052924/69‑1 (MQ=255)
                                                           gTTTTGTCACCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTGGCTTTTGAAATGGCGAGACAGAACtt       <  1:1517310/69‑1 (MQ=255)
                                                           gTTTTGTCACCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTGGCTTTTGAAATGGCGAGACAGAACtt       <  1:3350133/69‑1 (MQ=255)
                                                           gTTTTGTCACCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTGGCTTTTGAAATGGCGAGACAGAACtt       <  1:3346284/69‑1 (MQ=255)
                                                           gTTTTGTCACCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTGGCTTTTGAAATGGCGAGACAGAACtt       <  1:2188741/69‑1 (MQ=255)
                                                           gTTTTGTCACCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTGGCTTTTGAAATGGCGAGACAGAACtt       <  1:2355288/69‑1 (MQ=255)
                                                            ttttGTCACCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTGGCTTTTGAAATGGCGAGACAGAACttt      <  1:2459936/69‑1 (MQ=255)
                                                            ttttGTCACCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTGGCTTTTGAAATGGCGAGACAGAACttt      <  1:2451104/69‑1 (MQ=255)
                                                            ttttGTCACCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTGGCTTTTGAAATGGCGAGACAGAACttt      <  1:3418895/69‑1 (MQ=255)
                                                            ttttGTCACCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTGGCTTTTGAAATGGCGAGACAGAACttt      <  1:492399/69‑1 (MQ=255)
                                                            ttttGTCACCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTGGCTTTTGAAATGGCGAGACAGAACttt      <  1:1943419/69‑1 (MQ=255)
                                                            ttttGTCACCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTGGCTTTTGAAATGGCGAGACAGAACttt      <  1:575116/69‑1 (MQ=255)
                                                            ttttGTCACCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTGGCTTTTGAAATGGCGAGACAGAACttt      <  1:739866/69‑1 (MQ=255)
                                                                 tCATCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTGGCTTTCGAAATGGCGGGACAGAACTTTACTg  <  1:2677622/68‑1 (MQ=255)
                                                                 tCATCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTGGCTTTCGAAATGGCGGGACAGAACTTTACTg  <  1:1055586/68‑1 (MQ=255)
                                                                 tCATCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTGGCTTTCGAAATGGCGGGACAGAACTTTACTg  <  1:821324/68‑1 (MQ=255)
                                                                 tCATCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTGGCTTTCGAAATGGCGGGACAGAACTTTACTg  <  1:3053612/68‑1 (MQ=255)
                                                                 tCATCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTGGCTTTCGAAATGGCGGGACAGAACTTTACTg  <  1:772408/68‑1 (MQ=255)
                                                                 tCATCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTGGCTTTCGAAATGGCGGGACAGAACTTTACTg  <  1:1886000/68‑1 (MQ=255)
                                                                 tCATCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTGGCTTTCGAAATGGCGGGACAGAACTTTACTg  <  1:1932601/68‑1 (MQ=255)
                                                                 tCATCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTGGCTTTCGAAATGGCGGGACAGAACTTTACTg  <  1:481236/68‑1 (MQ=255)
                                                                 tCATCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTGGCTTTCGAAATGGCGGGACAGAACTTTACTg  <  1:2259426/68‑1 (MQ=255)
                                                                 tCATCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTGGCTTTCGAAATGGCGGGACAGAACTTTACTg  <  1:2009857/68‑1 (MQ=255)
                                                                 tCATCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTGGCTTTCGAAATGGCGGGACAGAACTTTACTg  <  1:2042406/68‑1 (MQ=255)
                                                                 tCATCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTGGCTTTCGAAATGGCGGGACAGAACTTTACTg  <  1:2096512/68‑1 (MQ=255)
                                                                    |                                                                
AGCGAATCATATATCTTCGCCAAAGCGGCCCATGCGCCATTTATTTCGCATCCGGCCGAGTTTTGTCACCTGCTGGTGGCGTTGAAGCAGAGGGTGTAGGTGGCTTTTGAAATGGCGAGACAGAACTTTACTG  >  minE/2676924‑2677056

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