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 858,231 T→A 52.3% Q170L (CAG→CTG)  trpC ← fused indole‑3‑glycerolphosphate synthetase and N‑(5‑phosphoribosyl)anthranilate isomerase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE858,2310TA52.3% 8.1 / 101.6 86Q170L (CAG→CTG) trpCfused indole‑3‑glycerolphosphate synthetase and N‑(5‑phosphoribosyl)anthranilate isomerase
Reads supporting (aligned to +/- strand):  ref base T (16/25);  new base A (26/19);  total (42/44)
Fisher's exact test for biased strand distribution p-value = 9.01e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCGACAAATCACGCAGATCGCGGTTGTTGATGCCAACGACCTTTGCTCCCAATGCAATGGCGCGCTCCTGTTCCTCTTCATTACTGACTTCGGTCAGCACCCCCATCTCCAGACTGTGAGCGACG  >  minE/858163‑858287
                                                                    |                                                        
tCGACAAATCACGCAGATCGCGGTTGTTGATGCCAACGACCTTTGCTCCCAATGCAATGGCGCGCTCCt                                                          >  1:519179/1‑69 (MQ=255)
tCGACAAATCACGCAGATCGCGGTTGTTGATGCCAACGACCTTTGCTCCCAATGCAATGGCGCGCTCCt                                                          >  1:1695814/1‑69 (MQ=255)
tCGACAAATCACGCAGATCGCGGTTGTTGATGCCAACGACCTTTGCTCCCAATGCAATGGCGCGCTCCt                                                          >  1:2305717/1‑69 (MQ=255)
tCGACAAATCACGCAGATCGCGGTTGTTGATGCCAACGACCTTTGCTCCCAATGCAATGGCGCGCTCCt                                                          >  1:2302379/1‑69 (MQ=255)
tCGACAAATCACGCAGATCGCGGTTGTTGATGCCAACGACCTTTGCTCCCAATGCAATGGCGCGCTCCt                                                          >  1:1189341/1‑69 (MQ=255)
tCGACAAATCACGCAGATCGCGGTTGTTGATGCCAACGACCTTTGCTCCCAATGCAATGGCGCGCTCCt                                                          >  1:806499/1‑69 (MQ=255)
tCGACAAATCACGCAGATCGCGGTTGTTGATGCCAACGACCTTTGCTCCCAATGCAATGGCGCGCTCCt                                                          >  1:1808778/1‑69 (MQ=255)
tCGACAAATCACGCAGATCGCGGTTGTTGATGCCAACGACCTTTGATCCCAATGCAATGGCGCGCTCCt                                                          >  1:2846452/1‑69 (MQ=255)
  gACAAATCACGCAGATCGCGGTTGTTGATGCCAACGACCTTTGCTCCCAATGCAATGGCGCGCTCCTGt                                                        >  1:457611/1‑69 (MQ=255)
  gACAAATCACGCAGATCGCGGTTGTTGATGCCAACGACCTTTGCTCCCAATGCAATGGCGCGCTCCTGt                                                        >  1:3525/1‑69 (MQ=255)
  gACAAATCACGCAGATCGCGGTTGTTGATGCCAACGACCTTTGCTCCCAATGCAATGGCGCGCTCCTGt                                                        >  1:1469707/1‑69 (MQ=255)
  gACAAATCACGCAGATCGCGGTTGTTGATGCCAACGACCTTTGCTCCCAATGCAATGGCGCGCTCCTGt                                                        >  1:2835930/1‑69 (MQ=255)
  gACAAATCACGCAGATCGCGGTTGTTGATGCCAACGACCTTTGCTCCCAATGCAATGGCGCGCTCCTGt                                                        >  1:266330/1‑69 (MQ=255)
              aGATCGCGGTTGTTGATGCCAACGACCTTTGCTCCCAATGCAATGGCGCGCTCCTGTTCCTCTTCAtt                                             <  1:371915/68‑1 (MQ=255)
               gATCGCGGTTGTTGATGCCAACGACCTTTGCTCCCAATGCAATGGCGCGCTCCTGTTCCTCTTCAtt                                             <  1:1796099/67‑1 (MQ=255)
                            gATGCCAACGACCTTTGCCCCCAATGCAATGGCGCGCTCCAGTTCCTCTTCATTACTGACTTCGGTCAg                              <  1:2821312/69‑1 (MQ=255)
                            gATGCCAACGACCTTTGCCCCCAATGCAATGGCGCGCTCCAGTTCCTCTTCATTACTGACTTCGGTCAg                              <  1:2113935/69‑1 (MQ=255)
                            gATGCCAACGACCTTTGCCCCCAATGCAATGGCGCGCTCCAGTTCCTCTTCATTACTGACTTCGGTCAg                              <  1:2259862/69‑1 (MQ=255)
                            gATGCCAACGACCTTTGCCCCCAATGCAATGGCGCGCTCCAGTTCCTCTTCATTACTGACTTCGGTCAg                              <  1:1646828/69‑1 (MQ=255)
                            gATGCCAACGACCTTTGCCCCCAATGCAATGGCGCGCTCCAGTTCCTCTTCATTACTGACTTCGGTCAg                              <  1:2374418/69‑1 (MQ=255)
                            gATGCCAACGACCTTTGCCCCCAATGCAATGGCGCGCTCCAGTTCCTCTTCATTACTGACTTCGGTCAg                              <  1:250883/69‑1 (MQ=255)
                            gATGCCAACGACCTTTGCCCCCAATGCAATGGCGCGCTCCAGTTCCTCTTCATTACTGACTTCGGTCAg                              <  1:1157826/69‑1 (MQ=255)
                            gATGCCAACGACCTTTGCCCCCAATGCAATGGCGCGCTCCAGTTCCTCTTCATTACTGACTTCGGTCAg                              <  1:715819/69‑1 (MQ=255)
                            gATGCCAACGACCTTTGCCCCCAATGCAATGGCGCGCTCCAGTTCCTCTTCATTACTGACTTCGGTCAg                              <  1:1482848/69‑1 (MQ=255)
                            gATGCCAACGACCTTTGCCCCCAATGCAATGGCGCGCTCCAGTTCCTCTTCATTACTGACTTCGGTCAg                              <  1:1533434/69‑1 (MQ=255)
                            gATGCCAACGACCTTTGCCCCCAATGCAATGGCGCGCTCCAGTTCCTCTTCATTACTGACTTCGGTCAg                              <  1:1064976/69‑1 (MQ=255)
                            gATGCCAACGACCTTTGCCCCCAATGCAATGGCGCGCTCCAGTTCCTCTTCATTACTGACTTCGGTCAg                              <  1:868557/69‑1 (MQ=255)
                            gATGCCAACGACCTTTGCCCCCAATGCAATGGCGCGCTCCAGTTCCTCTTCATTACTGACTTCGGTCAg                              <  1:81064/69‑1 (MQ=255)
                             aTGCCAACGACCTTTGCCCCCAATGCAATGGCGCGCTCCAGTTCCTCTTCATTACTGACTTCGGTCAg                              <  1:1123342/68‑1 (MQ=255)
                             aTGCCAACGACCTTTGCCCCCAATGCAATGGCGCGCTCCAGTTCCTCTTCATTACTGACTTCGGTCAg                              <  1:359519/68‑1 (MQ=255)
                             aTGCCAACGACCTTTGCCCCCAATGCAATGGCGCGCTCCAGTTCCTCTTCATTACTGACTTCGGTCAg                              <  1:2576644/68‑1 (MQ=255)
                              tGCCAACGACCTTTGCCCCCAATGCAATGGCGCGCTCCAGTTCCTCTTCATTACTGACTTCGGTCAg                              <  1:957271/67‑1 (MQ=255)
                               gCCAACGACCTTTGCTCCCAATGCAATGGCGCGCTCCTGTTCCTCTTCATTACTGACTTCGGTCAGCAc                           <  1:1555325/69‑1 (MQ=255)
                                 cAACGACCTTTGCGCCCAATGCAATGGCGCGCTCCAGTTCCTCTTCATTACTGACTTCg                                   >  1:1068323/1‑59 (MQ=39)
                                 cAACGACCTTTGCCCCCAATGCAATGGCGCGCTCCAGTTCCTCTTCATTACTGACttg                                    >  1:1779847/1‑57 (MQ=255)
                                 cAACGACCTTTGCCCCCAATGCAATGGCGCGCTCCAGTTCCTCTTCATTACTGACt                                      >  1:1499989/1‑56 (MQ=255)
                                 cAACGACCTTTGCCCCCAATGCAATGGCGCGCTCCAGTTCCTCTTCATTACTGACTTCg                                   >  1:985044/1‑59 (MQ=255)
                                 cAACGACCTTTGCCCCCAATGCAATGGCGCGCTCCAGTTCCTCTTCATTACTGACTTCg                                   >  1:2732382/1‑59 (MQ=255)
                                 cAACGACCTTTGCCCCCAATGCAATGGCGCGCTCCAGTTCCTCTTCATTACTGACTTCg                                   >  1:2451024/1‑59 (MQ=255)
                                 cAACGACCTTTGCCCCCAATGCAATGGCGCGCTCCAGTTCCTCTTCATTACTGACTTCg                                   >  1:2741805/1‑59 (MQ=255)
                                 cAACGACCTTTGCCCCCAATGCAATGGCGCGCTCCAGTTCCTCTTCATTACTGACTTCg                                   >  1:2768817/1‑59 (MQ=255)
                                 cAACGACCTTTGCCCCCAATGCAATGGCGCGCTCCAGTTCCTCTTCATTACTGACTTCg                                   >  1:925355/1‑59 (MQ=255)
                                 cAACGACCTTTGCCCCCAATGCAATGGCGCGCTCCAGTTCCTCTTCATTACTGACTTCg                                   >  1:915499/1‑59 (MQ=255)
                                 cAACGACCTTTGCCCCCAATGCAATGGCGCGCTCCAGTTCCTCTTCATTACTGACTTCg                                   >  1:897796/1‑59 (MQ=255)
                                 cAACGACCTTTGCCCCCAATGCAATGGCGCGCTCCAGTTCCTCTTCATTACTGACTTCg                                   >  1:3173391/1‑59 (MQ=255)
                                 cAACGACCTTTGCCCCCAATGCAATGGCGCGCTCCAGTTCCTCTTCATTACTGACTTCg                                   >  1:3200215/1‑59 (MQ=255)
                                 cAACGACCTTTGCCCCCAATGCAATGGCGCGCTCCAGTTCCTCTTCATTACTGACTTCg                                   >  1:3288823/1‑59 (MQ=255)
                                 cAACGACCTTTGCCCCCAATGCAATGGCGCGCTCCAGTTCCTCTTCATTACTGACTTCg                                   >  1:726506/1‑59 (MQ=255)
                                 cAACGACCTTTGCCCCCAATGCAATGGCGCGCTCCAGTTCCTCTTCATTACTGACTTCg                                   >  1:1385911/1‑59 (MQ=255)
                                 cAACGACCTTTGCCCCCAATGCAATGGCGCGCTCCAGTTCCTCTTCATTACTGACTTCg                                   >  1:1695362/1‑59 (MQ=255)
                                 cAACGACCTTTGCCCCCAATGCAATGGCGCGCTCCAGTTCCTCTTCATTACTGACTTCg                                   >  1:1698981/1‑59 (MQ=255)
                                 cAACGACCTTTGCCCCCAATGCAATGGCGCGCTCCAGTTCCTCTTCATTACTGACTTCg                                   >  1:1554214/1‑59 (MQ=255)
                                 cAACGACCTTTGCCCCCAATGCAATGGCGCGCTCCAGTTCCTCTTCATTACTGACTTCg                                   >  1:1488693/1‑59 (MQ=255)
                                 cAACGACCTTTGCCCCCAATGCAATGGCGCGCTCCAGTTCCTCTTCATTACTGACTTCg                                   >  1:1447813/1‑59 (MQ=255)
                                 cAACGACCTTTGCCCCCAATGCAATGGCGCGCTCCAGTTCCTCTTCATTACTGACTTCg                                   >  1:1831092/1‑59 (MQ=255)
                                 cAACGACCTTTGCCCCCAATGCAATGGCGCGCTCCAGTTCCTCTTCATTACTGACTTCg                                   >  1:183521/1‑59 (MQ=255)
                                 cAACGACCTTTGCCCCCAATGCAATGGCGCGCTCCAGTTCCTCTTCATTACTGACTTCg                                   >  1:1894808/1‑59 (MQ=255)
                                 cAACGACCTTTGCCCCCAATGCAATGGCGCGCTCCAGTTCCTCTTCATTACTGACTTCg                                   >  1:1255990/1‑59 (MQ=255)
                                 cAACGACCTTTGCCCCCAATGCAATGGCGCGCTCCAGTTCCTCTTCATTACTGACTTCg                                   >  1:2417948/1‑59 (MQ=255)
                                     gACCTTTGCCCCCAATGCAATGGCGCGCTCCAGTTCCTCTTCATTACTGACTTCGGTCAg                              <  1:2127528/60‑1 (MQ=255)
                                         tttGCTCCCAATGCAATGGCGCTCTCCTGTTCCTCTTCATTACTGACTTCGGTc                                <  1:1480614/54‑1 (MQ=255)
                                         tttGCTCCCAATGCAATGGCGCGCTCCTGTTCCTCTTCATTACTGACTTCGGTc                                <  1:2743916/54‑1 (MQ=255)
                                         tttGCTCCCAATGCAATGGCGCGCTCCTGTTCCTCTTCATTACTGACTTCGGTc                                <  1:877592/54‑1 (MQ=255)
                                         tttGCTCCCAATGCAATGGCGCGCTCCTGTTCCTCTTCATTACTGACTTCGGTc                                <  1:1384588/54‑1 (MQ=255)
                                         tttGCTCCCAATGCAATGGCGCGCTCCTGTTCCTCTTCATTACTGACTTCGGTc                                <  1:1771945/54‑1 (MQ=255)
                                         tttGCTCCCAATGCAATGGCGCGCTCCTGTTCCTCTTCATTACTGACTTCGGTc                                <  1:769924/54‑1 (MQ=255)
                                         tttGCTCCCAATGCAATGGCGCGCTCCTGTTCCTCTTCATTACTGACTTCGGTc                                <  1:560933/54‑1 (MQ=255)
                                         tttGCTCCCAATGCAATGGCGCGCTCCTGTTCCTCTTCATTACTGACTTCGGTc                                <  1:1095409/54‑1 (MQ=255)
                                         tttGCTCCCAATGCAATGGCGCGCTCCTGTTCCTCTTCATTACTGACTTCGGTc                                <  1:1079306/54‑1 (MQ=255)
                                         tctGCTCCCAATGCAATGGCGCGCTCCTGTTCCTCTTCATTACTGACTTCGGTc                                <  1:2575096/52‑1 (MQ=255)
                                             cTCCCAATGCAATGGCGCGCTCCTGTTCCTCTTCATTACTGACTTCGGTCAGCACCCCCATCTCCAg               <  1:995933/67‑1 (MQ=255)
                                             cTCCCAATGCAATGGCGCGCTCCTGTTCCTCTTCATTACTGACTTCGGTCAGCACCCCCATCTCCAg               <  1:1404102/67‑1 (MQ=255)
                                             cTCCCAATGCAATGGCGCGCTCCTGTTCCTCTTCATTACTGACTTCGGTCAGCACCCCCATCTCCAg               <  1:104956/67‑1 (MQ=255)
                                             cTCCCAATGCAATGGCGCGCTCCTGTTCCTCTTCATTACTGACTTCGGTCAGCACCCCCATCTCCAg               <  1:3150375/67‑1 (MQ=255)
                                             cTCCCAATGCAATGGCGCGCTCCTGTTCCTCTTCATTACTGACTTCGGTCAGCACCCCCATCTCCAg               <  1:2510822/67‑1 (MQ=255)
                                             cTCCCAATGCAATGGCGCGCTCCTGTTCCTCTTCATTACTGACTTCGGTCAGCACCCCCATCTCCAg               <  1:2598396/67‑1 (MQ=255)
                                             cTCCCAATGCAATGGCGCGCTCCTGTTCCTCTTCATTACTGACTTCGGTCAGCACCCCCATCTCCAg               <  1:1876253/67‑1 (MQ=255)
                                             cTCCCAATGCAATGGCGCGCTCCTGTTCCTCTTCATTACTGACTTCGGTCAGCACCCCCATCTCCAg               <  1:1869511/67‑1 (MQ=255)
                                             cTCCCAATGCAATGGCGCGCTCCTGTTCCTCTTCATTACTGACTTCGGTCAGCACCCCCATCTCCAg               <  1:1744703/67‑1 (MQ=255)
                                             cTCCCAATGCAATGGCGCGCTCCTGTTCCTCTTCATTACTGACTTCGGTCAGCACCCCCATCTCCAg               <  1:347233/67‑1 (MQ=255)
                                             cTCCCAATGCAATGGCGCGCTCCTGTTCCTCTTCATTACTGACTTCGGTCAGCACCCCCATCTACAg               <  1:919370/67‑1 (MQ=255)
                                                  aatgcaatgGCGCGCTCCTGTTCCTCTTCATTACTGACTTCGGTCAGCAc                           <  1:2328058/50‑1 (MQ=255)
                                                      caatgGCGCGCTCCTGTTCCTCTTCATTACTGACTTCGGTCAGCACCCCCATCTCCAGACTGTGAGCGa    >  1:501938/1‑69 (MQ=255)
                                                        atgGCGCGCTCCTGTTCCTCTTCATTACTGACTTCGGTCAGCACCCCCATCTCCAGACTGTGAGCGAcg  >  1:721535/1‑69 (MQ=255)
                                                        atgGCGCGCTCCTGTTCCTCTTCATTACTGACTTCGGTCAGCACCCCCATCTCCAGACTGTGAGCGAcg  >  1:3180809/1‑69 (MQ=255)
                                                        atgGCGCGCTCCTGTTCCTCTTCATTACTGACTTCGGTCAGCACCCCCATCTCCAGACTGTGAGCGAcg  >  1:731232/1‑69 (MQ=255)
                                                        atgGCGCGCTCCTGTTCCTCTTCATTACTGACTTCGGTCAGCACCCCCATCTCCAGACTGTGAGCGAcg  >  1:3174731/1‑69 (MQ=255)
                                                        atgGCGCGCTCCTGTTCCTCTTCATTACTGACTTCGGTCAGCACCCCCATCTCCAGACTGTGAGCGAcg  >  1:1680858/1‑69 (MQ=255)
                                                        atgGCGCGCTCCTGTTCCTCTTCATTACTGACTTCGGTCAGCACCCCCATCTCCAGACTGTGAGCGAcg  >  1:1706036/1‑69 (MQ=255)
                                                        atgGCGCGCTCCTGTTCCTCTTCATTACTGACTTCGGTCAGCACCCCCATCTCCAGACTGTGAGCGAcg  >  1:2817930/1‑69 (MQ=255)
                                                        atgGCGCGCTCCTGTTCCTCTTCATTACTGACTTCGGTCAGCACCCCCATCTCCAGACTGTGAGCGAcg  >  1:2560274/1‑69 (MQ=255)
                                                        atgGCGCGCTCCTGTTCCTCTTCATTACTGACTTCGGTCAGCACCCCCATCTCCAGACTGTGAGCGAc   >  1:2561732/1‑68 (MQ=255)
                                                        atgGCGCGCTCCTGTTCCTCTTCATTACTGACTTCGGTCAGCACCCCCATCTACAGACTGTGAGCGAcg  >  1:1524420/1‑69 (MQ=255)
                                                        atgGCGCGCTCCAGTTCCTCTTCATTACTGACTTCGGTCAg                              <  1:1270469/41‑1 (MQ=255)
                                                                    |                                                        
TCGACAAATCACGCAGATCGCGGTTGTTGATGCCAACGACCTTTGCTCCCAATGCAATGGCGCGCTCCTGTTCCTCTTCATTACTGACTTCGGTCAGCACCCCCATCTCCAGACTGTGAGCGACG  >  minE/858163‑858287

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