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 686,819 T→C 30.1% F19F (TTT→TTC)  yccX → predicted acylphosphatase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE686,8190TC30.1% 66.1 / 33.4 73F19F (TTT→TTC) yccXpredicted acylphosphatase
Reads supporting (aligned to +/- strand):  ref base T (27/24);  new base C (10/12);  total (37/36)
Fisher's exact test for biased strand distribution p-value = 6.16e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.54e-01

GAGAGCAGCAATGTCGAAAGTCTGCATAATTGCCTGGGTTTACGGGCGAGTTCAGGGCGTAGGATTTCGCTACACCACACAGTACGAAGCGAAAAGACTGGGTTTAACCGGGTACGCCAAAAATCTTGACGAT  >  minE/686753‑686885
                                                                  |                                                                  
gagaGCAGCAATGTCGAAAGTCTGCATAATTGCCTGGGTTTACGGGCGAGTTCAGGGCGTAGGATTTc                                                                   >  1:3157271/1‑68 (MQ=255)
gagaGCAGCAATGTCGAAAGTCTGCATAATTGCCTGGGTTTACGGGCGAGTTCAGGGCGTAGGATTTc                                                                   >  1:1101973/1‑68 (MQ=255)
gagaGCAGCAATGTCGAAAGTCTGCATAATTGCCTGGGTTTACGGGCGAGTTCAGGGCGTAGGATTTc                                                                   >  1:197119/1‑68 (MQ=255)
 agagCAGCAATGTCGAAAGTCTGCATAATTGCCTGGGTTTACGGGCGAGTTCAGGGCGTAGGATTTCGc                                                                 <  1:1998994/69‑1 (MQ=255)
 agagCAGCAATGTCGAAAGTCTGCATAATTGCCTGGGTTTACGGGCGAGTTCAGGGCGTAGGATTTCGc                                                                 <  1:3162949/69‑1 (MQ=255)
 agagCAGCAATGTCGAAAGTCTGCATAATTGCCTGGGTTTACGGGCGAGTTCAGGGCGTAGGATTTCGc                                                                 <  1:262300/69‑1 (MQ=255)
 agagCAGCAATGTCGAAAGTCTGCATAATTGCCTGGGTTTACGGGCGAGTTCAGGGCGTAGGATTTCGc                                                                 <  1:13288/69‑1 (MQ=255)
 agagCAGCAATGTCGAAAGTCTGCATAATTGCCTGGGTTTACGGGCGAGTTCAGGGCGTAGGATTCCGc                                                                 <  1:2729397/69‑1 (MQ=255)
 agagCAGCAATGTCGAAAGTCTGCATAATTGCCTGGGTTTACGGGCGAGTTCAGGGCGTAGGATTCCGc                                                                 <  1:3231512/69‑1 (MQ=255)
 agagCAGCAATGTCGAAAGTCTGCATAATTGCCTGGGTTTACGGGCGAGTTCAGGGCGTAGGATTCCGc                                                                 <  1:2826367/69‑1 (MQ=255)
 agagCAGCAATGTCGAAAGTCTGCATAATTGCCTGGGTTTACGGGCGAGTTCAGGGCGTAGGATTCCGc                                                                 <  1:103423/69‑1 (MQ=255)
 agagCAGCAATGTCGAAAGTCTGCATAATTGCCTGGGTTTACGGGCGAGTTCAGGGCGTAGGATTCCGc                                                                 <  1:2836817/69‑1 (MQ=255)
 agagCAGCAATGTCGAAAGTCTGCATAATTGCCTGGGTTTACGGGCGAGTTCAGGGCGTAGGATTCCGc                                                                 <  1:2949260/69‑1 (MQ=255)
 agagCAGCAATGTCGAAAGTCTGCATAATTGCCTGGGTTTACGGGCGAGTTCAGGGCGTAGGATTCCGc                                                                 <  1:1967421/69‑1 (MQ=255)
 agagCAGCAATGTCGAAAGTCTGCATAATTGCCTGGGTTTACGGGCGAGTTCAGGGCGTAGGATTCCGc                                                                 <  1:3197406/69‑1 (MQ=255)
 agagCAGCAATGTCGAAAGTCTGCATAATTGCCTGGGTTTACGGGCGAGTTCAGGGCGTAGGATTCCGc                                                                 <  1:423777/69‑1 (MQ=255)
 agagCAGCAATGTCGAAAGTCTGCATAATTGCCTGGGTTTACGGGCGAGTTCAGGGCGTAGGATTCCGc                                                                 <  1:563695/69‑1 (MQ=255)
  gagCAGCAATGTCGAAAGTCTGCATAATTGCCTGGGTTTACGGGCGAGTTCAGGGCGTAGGATTCCGc                                                                 <  1:800222/68‑1 (MQ=255)
   agcagcAATGTCGAAAGTCTGCATAATTGCCTGGGTTTACGGGCGAGTTCAGGGCGTAGGATTTCGc                                                                 <  1:1323017/67‑1 (MQ=255)
   agcagcAATGTCGAAAGTCTGCATAATTGCCTGGGTTTACGGGCGAGTTCAGGGCGTAGGATTTCGCTa                                                               <  1:1827082/69‑1 (MQ=255)
   agcagcAATGTCGAAAGTCTGCATAATTGCCTGGGTTTACGGGCGAGTTCAGGGCGTAGGATTTCGCTa                                                               <  1:1589088/69‑1 (MQ=255)
   agcagcAATGTCGAAAGTCTGCATAATTGCCTGGGTTTACGGGCGAGTTCAGGGCGTAGGATTTCGCTa                                                               <  1:3099412/69‑1 (MQ=255)
   agcagcAATGTCGAAAGTCTGCATAATTGCCTGGGTTTACGGGCGAGTTCAGGGCGTAGGATTTCGCTa                                                               <  1:2688640/69‑1 (MQ=255)
   agcagcAATGTCGAAAGTCTGCATAATTGCCTGGGTTTACGGGCGAGTTCAGGGCGTAGGATTTCGCTa                                                               <  1:34501/69‑1 (MQ=255)
        caATGTCGAAAGTCTGCATAATTGCCTGGGTTTACGGGCGAGTTCAGGGCGTAGGATTTCGCTAcacca                                                          <  1:1723173/69‑1 (MQ=255)
        caATGTCGAAAGTCTGCATAATTGCCTGGGTTTACGGGCGAGTTCAGGGCGTAGGATTTCGCTAcacca                                                          <  1:1138540/69‑1 (MQ=255)
        caATGTCGAAAGTCTGCATAATTGCCTGGGTTTACGGGCGAGTTCAGGGCGTAGGATTTCGCTAcacca                                                          <  1:3432973/69‑1 (MQ=255)
        caATGTCGAAAGTCTGCATAATTGCCTGGGTTTACGGGCGAGTTCAGGGCGTAGGATTTCGCTAcacca                                                          <  1:2296991/69‑1 (MQ=255)
        caATGTCGAAAGTCTGCATAATTGCCTGGGTTTACGGGCGAGTTCAGGGCGTAGGATTTCGCTAcacca                                                          <  1:1100890/69‑1 (MQ=255)
                  aGTCTGCATAATTGCCTGGGTTTACGGGCGAGTTCAGGGCGTAGGATTTCGCTACACCACACAGTACGa                                                >  1:1444469/1‑69 (MQ=255)
                    tCTGCATAATTGGCTGGGTTTACGGGCGAGTTCAGGGCGTAGGTTTCCGc                                                                 <  1:1935488/50‑1 (MQ=255)
                      tGCATAATTGCCTGGGTTTACGGGCGAGTTCAGGGCGTAGGATTTCGCTACACCACACAGTACGAAGCg                                            <  1:91893/69‑1 (MQ=255)
                            aTTGCCTGGGTTTACGGGCGAGTTCAGGGCGTAGGATTTCGCTa                                                               >  1:1508676/1‑44 (MQ=255)
                            aTTGCCTGGGTTTACGGGCGAGTTCAGGGCGTAGGATTTCGCTa                                                               >  1:1512532/1‑44 (MQ=255)
                            aTTGCCTGGGTTTACGGGCGAGTTCAGGGCGTAGGATTTCGCTACACCACACAGTACGAAGCGAAAAg                                       >  1:1752573/1‑68 (MQ=255)
                            aTTGCCTGGGTTTACGGGCGAGTTCAGGGCGTAGGATTTCGCTACACCACACAGTACGAAGCGAAAAGa                                      >  1:1323544/1‑69 (MQ=255)
                            aTTGCCTGGGTTTACGGGCGAGTTCAGGGCGTAGGATTTCGCTACACCACACAGTACGAAGCGAAAAGa                                      >  1:535359/1‑69 (MQ=255)
                            aTTGCCTGGGTTTACGGGCGAGTTCAGGGCGTAGGATTTCGCTACACCACACAGTACGAAGCGAAAAGa                                      >  1:3212931/1‑69 (MQ=255)
                            aTTGCCTGGGTTTACGGGCGAGTTCAGGGCGTAGGATTTCGCTACACCACACAGTACGAAGCGAAAAGa                                      >  1:2050893/1‑69 (MQ=255)
                            aTTGCCTGGGTTTACGGGCGAGTTCAGGGCGTAGGATTTCGCTACACCACACAGTACGAAGCGAAAAGa                                      >  1:568063/1‑69 (MQ=255)
                                      tttACGGGCGAGTTCAGGGCGTAGGATTTCGCTACACCACACAGTACGAAGCGAAAAGACTGGGTTTa                             <  1:2265723/68‑1 (MQ=255)
                                       ttACGGGCGAGTTCAGGGCGTAGGATTCCGCTACCCCACGCAGTACGAAGCGAAAAAACTGGGACTAAc                           >  1:2228387/1‑69 (MQ=255)
                                       ttACGGGCGAGTTCAGGGCGTAGGATTCCGCTACACCACGCAGTACGAAGCGAAAAAACTGGGACTAAc                           >  1:2926001/1‑69 (MQ=255)
                                       ttACGGGCGAGTTCAGGGCGTAGGATTCCGCTACACCACGCAGTACGAAGCGAAAAAACTGGGACTAAc                           >  1:109997/1‑69 (MQ=255)
                                       ttACGGGCGAGTTCAGGGCGTAGGATTCCGCTACACCACGCAGTACGAAGCGAAAAAACTGGGACTAAc                           >  1:2703240/1‑69 (MQ=255)
                                       ttACGGGCGAGTTCAGGGCGTAGGATTCCGCTACACCACGCAGTACGAAGCGAAAAAACTGGGACTAAc                           >  1:2537908/1‑69 (MQ=255)
                                       ttACGGGCGAGTTCAGGGCGTAGGATTCCGCTACACCACGCAGTACGAAGCGAAAAAACTGGGACTAAc                           >  1:2519649/1‑69 (MQ=255)
                                       ttACGGGCGAGTTCAGGGCGTAGGATTCCGCTACACCACGCAGTACGAAGCGAAAAAACTGGGACTAAc                           >  1:2474217/1‑69 (MQ=255)
                                       ttACGGGCGAGTTCAGGGCGTAGGATTCCGCTACACCACGCAGTACGAAGCGAAAAAACTGGGACTAAc                           >  1:38093/1‑69 (MQ=255)
                                       ttACGGGCGAGTTCAGGGCGTAGGATTCCGCTACACCACGCAGTACGAAGCGAAAAAACTGGGACTAAc                           >  1:598706/1‑69 (MQ=255)
                                       ttACGGGCGAGTTCAGGGCGTAGGATTCCGCTACACCACGCAGTACGAAGCGAAAAAACTGGGACTAAc                           >  1:1247454/1‑69 (MQ=255)
                                        tACGGGCGAGTTCAGGGCGTAGGATTTCGCTacac                                                            >  1:1292457/1‑35 (MQ=255)
                                        tACGGGCGAGTTCAGGGCGTAGGATTTCGCTACACCACACAGTACGAAGCGAAAAGACTGGGtt                               >  1:2648757/1‑64 (MQ=255)
                                        tACGGGCGAGTTCAGGGCGTAGGATTTCGCTACACCACACAGTACGAAGCGAAAAGACTGGGTTTAAcc                          >  1:2644823/1‑69 (MQ=255)
                                        tACGGGCGAGTTCAGGGCGTAGGATTTCGCTACACCACACAGTACGAAGCGAAAAGACTGGGTTTAAcc                          >  1:1554085/1‑69 (MQ=255)
                                        tACGGGCGAGTTCAGGGCGTAGGATTTCGCTACACAACACAGTACGAAGCGAAAAGACTGGGTTTAAcc                          >  1:1748363/1‑69 (MQ=255)
                                            ggCGAGTTCAGGGCGTAGGATTTCGCTACACCACACAGTACGAAGCGAAAAGACTGGGTTTAACCggg                       <  1:1168646/68‑1 (MQ=255)
                                                    cAGGGCGTAGGATTTCGCTACACCACACAGTACGAAGCGAAAAg                                       <  1:3117651/44‑1 (MQ=255)
                                                    cAGGGCGTAGGATTTCGCTACACCACACAGTACGAAGCGAAAAg                                       <  1:97884/44‑1 (MQ=255)
                                                    cAGGGCGTAGGATTTCGCTACACCACACAGTACGAAGCGAAAAg                                       >  1:1617405/1‑44 (MQ=255)
                                                    cAGGGCGTAGGATTTCGCTACACCACACAGTACGAAGCGAAAAg                                       >  1:574002/1‑44 (MQ=255)
                                                    cAGGGCGTAGGATTTCGCTACACCACACAGTACGAAGCGAAAAg                                       >  1:1728524/1‑44 (MQ=255)
                                                    cAGGGCGTAGGATTTCGCTACACCACACAGTACGAAGCGAAAAg                                       >  1:1900144/1‑44 (MQ=255)
                                                    cAGGGCGTAGGATTTCGCTACACCACACAGTACGAAGCGAAAAg                                       >  1:2230323/1‑44 (MQ=255)
                                                    cAGGGCGTAGGATTTCGCTACACCACACAGTACGAAGCGAAAAg                                       <  1:226957/44‑1 (MQ=255)
                                                    cAGGGCGTAGGATTTCGCTACACCACACAGTACGAAGCGAAAAg                                       >  1:2822463/1‑44 (MQ=255)
                                                    cAGGGCGTAGGATTTCGCTACACCACACAGTACGAAGCGAAAAGACTGGGTTTAACCGGGTACGCCaaa              >  1:2801235/1‑69 (MQ=255)
                                                    cAGGGCGTAGGATTTCGCTACACCACACAGTACGAAGCGAAAAGACTGGGTTTAACCGGGTACGCCaaa              >  1:918662/1‑69 (MQ=255)
                                                    cAGGGCGTAGGATTTCGCTACACCACACAGTACGAAGCGAAAAGACTGGGTTTAACCGGGAACGCCaaa              >  1:2866275/1‑69 (MQ=255)
                                                             ggATTTCGCTACACCACACAGTACGAAGCGAAAAGACTGGGTTTAACCGGGTACGCCAAAAATCTTGAc     <  1:3324400/69‑1 (MQ=255)
                                                             ggATTTCGCTACACCACACAGTACGAAGCGAAAAGACTGGGTTTAACCGGGTACGCCAAAAATCTTGAc     >  1:1674231/1‑69 (MQ=255)
                                                             ggATTTCGCTACACCACACAGTACGAAGCGAAAAGACTGGGTTTAACCGGGTACGCCAAAAATCTTGAc     <  1:3247343/69‑1 (MQ=255)
                                                             ggATTTCGCTACACCACACAGTACGAAGCGAAAAGACTGGGTTTAACCGGGTACGCCAAAAATCTTGAc     <  1:3242674/69‑1 (MQ=255)
                                                                tttCGCTACACCACACAGTACGAAGCGAAAAGACTGGGTTTAACCGGGTACGCCAAAAATCTTGACGAt  >  1:641945/1‑69 (MQ=255)
                                                                tttCGCTACACCACACAGTACGAAGCGAAAAGACTGGGTTTAACCGGGTACGCCAAAAATCTTGACGAt  >  1:3145046/1‑69 (MQ=255)
                                                                tttCGCGACACCACACAGTACGAAGCGAAAAGACTGGGTTTAACCGGGTACGCCAAAAATCTTGACGAt  >  1:436282/1‑69 (MQ=255)
                                                                  |                                                                  
GAGAGCAGCAATGTCGAAAGTCTGCATAATTGCCTGGGTTTACGGGCGAGTTCAGGGCGTAGGATTTCGCTACACCACACAGTACGAAGCGAAAAGACTGGGTTTAACCGGGTACGCCAAAAATCTTGACGAT  >  minE/686753‑686885

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