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 1,960,780 C→T 76.1% A223A (GCG→GCA)  pgk ← phosphoglycerate kinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,960,7800CT76.1% 58.2 / 14.4 50A223A (GCG→GCA) pgkphosphoglycerate kinase
Reads supporting (aligned to +/- strand):  ref base C (10/2);  new base T (21/17);  total (31/19)
Fisher's exact test for biased strand distribution p-value = 1.00e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAGACGTTTAGCTTCGTCAACCAGGTCAGCTTCGTACAGGGATTTACCCACATCGTGGCCTTGTGCCGCGATAAAGGTGTTAGCGATACCACCACCAACAATCAGCTGGTCAGCGATTTTAGACAGGGA  >  minE/1960714‑1960842
                                                                  |                                                              
cagACGTTTAGCTTCGTCAACCAGGTCAGCTTCGTACAGGGATTTACCCACATCGTGGCCTTGtgctgc                                                              <  1:300227/69‑1 (MQ=255)
cagACGTTTAGCTTCGTCAACCAGGTCAGCTTCGTACAGGGATTTACCCACATCGTGGCCTTGtgctgc                                                              <  1:1860226/69‑1 (MQ=255)
cagACGTTTAGCTTCGTCAACCAGGTCAGCTTCGTACAGGGATTTACCCACATCGTGGCCTTGtgctgc                                                              <  1:1959552/69‑1 (MQ=255)
cagACGTTTAGCTTCGTCAACCAGGTCAGCTTCGTACAGGGATTTACCCACATCGTGGCCTTGtgctgc                                                              <  1:1707239/69‑1 (MQ=255)
cagACGTTTAGCTTCGTCAACCAGGTCAGCTTCGTACAGGGATTTACCCACATCGTGGCCTTGtgctgc                                                              <  1:1970826/69‑1 (MQ=255)
cagACGTTTAGCTTCGTCAACCAGGTCAGCTTCGTACAGGGATTTACCCACATCGTGGCCTTGtgctgc                                                              <  1:1674263/69‑1 (MQ=255)
cagACGTTTAGCTTCGTCAACCAGGTCAGCTTCGTACAGGGATTTACCCACATCGTGGCCTTGtgctgc                                                              <  1:1644920/69‑1 (MQ=255)
cagACGTTTAGCTTCGTCAACCAGGTCAGCTTCGTACAGGGATTTACCCACATCGTGGCCTTGtgctgc                                                              <  1:2419304/69‑1 (MQ=255)
cagACGTTTAGCTTCGTCAACCAGGTCAGCTTCGTACAGGGATTTACCCACATCGTGGCCTTGtgctgc                                                              <  1:3139373/69‑1 (MQ=255)
cagACGTTTAGCTTCGTCAACCAGGTCAGCTTCGTACAGGGATTTACCCACATCGTGGCCTTGtgctgc                                                              <  1:1465485/69‑1 (MQ=255)
cagACGTTTAGCTTCGTCAACCAGGTCAGCTTCGTACAGGGATTTACCCACATCGTGGCCTTGtgctgc                                                              <  1:1431573/69‑1 (MQ=255)
cagACGTTTAGCTTCGTCAACCAGGTCAGCTTCGTACAGGGATTTACCCACATCGTGGCCTTGtgctgc                                                              <  1:3193485/69‑1 (MQ=255)
cagACGTTTAGCTTCGTCAACCAGGTCAGCTTCGTACAGGGATTTACCCACATCGTGGCCTTGtgctgc                                                              <  1:3257747/69‑1 (MQ=255)
cagACGTTTAGCTTCGTCAACCAGGTCAGCTTCGTACAGGGATTTACCCACATCGTGGCCTTGtgctgc                                                              <  1:3320645/69‑1 (MQ=255)
cagACGTTTAGCTTCGTCAACCAGGTCAGCTTCGTACAGGGATTTACCCACATCGTGGCCTTGtgctgc                                                              <  1:1157941/69‑1 (MQ=255)
cagACGTTTAGCTTCGTCAACCAGGTCAGCTTCGTACAGGGATTTACCCACATCGTGGCCTTGtgctgc                                                              <  1:57494/69‑1 (MQ=255)
cagACGTTTAGCTTCGTCAACCAGGTCAGCTTCGTACAGGGATTTACCCACATCGTGGCCTTGtgctgc                                                              <  1:816092/69‑1 (MQ=255)
cagACGTTTAGCTTCGTCAACCAGGTCAGCTTCGTACAGGGATTTACCCACATCGTGGCCTTGtgctgc                                                              <  1:999980/69‑1 (MQ=255)
cagACGTTTAGCTTCGTCAACCAGGTCAGCTTCGTACAGGGATTTACCCACATCGTGGCCTTGTGCcgc                                                              >  1:2595347/1‑69 (MQ=255)
cagACGTTTAGCTTCGTCAACCAGGTCAGCTTCGTACAGGGATTTACCCACATCGTGGCCTTGTGCcgc                                                              >  1:28905/1‑69 (MQ=255)
cagACGTTTAGCTTCGTCAACCAGGTCAGCTTCGTACAGGGATTTACCCACATCGTGGCCTTGTGCcgc                                                              >  1:2479073/1‑69 (MQ=255)
cagACGTTTAGCTTCGTCAACCAGGTCAGCTTCGTACAGGGATTTACCCACATCGTGGCCTTGTGCcgc                                                              >  1:2357614/1‑69 (MQ=255)
cagACGTTTAGCTTCGTCAACCAGGTCAGCTTCGTACAGGGATTTACCCACATCGTGGCCTTGTGCcgc                                                              >  1:1284487/1‑69 (MQ=255)
cagACGTTTAGCTTCGTCAACCAGGTCAGCTTCGTACAGGGATTTACCCACATCGTGGCCTTGTGCcgc                                                              >  1:1564278/1‑69 (MQ=255)
cagACGTTTAGCTTCGTCAACCAGGTCAGCTTCGTACAGGGATTTACCCACATCGTGGCCTTGTGCcg                                                               >  1:673617/1‑68 (MQ=255)
         aGCTTCGTCAACCAGGTCAGCTTCGTACAGGGATTTACCCACATCGTGGCCTTGtgctgc                                                              <  1:759172/60‑1 (MQ=255)
                  aaCCAGGTCAGCTTCGTACAGGGATTTACCCACATCGTGGCCTTGtgctgc                                                              <  1:611378/51‑1 (MQ=255)
                      aGGTCAGCTTCGTACAGGGATTTACCCACATCGTGGCCTTGtgctgc                                                              <  1:1514308/47‑1 (MQ=255)
                               tCGTACAGGGATTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACcaacg                               >  1:2225184/1‑68 (MQ=255)
                               tCGTACAGGGATTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACcaacg                               >  1:1691727/1‑68 (MQ=255)
                               tCGTACAGGGATTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACcaacg                               >  1:3220679/1‑68 (MQ=255)
                               tCGTACAGGGATTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACcaacg                               >  1:2466392/1‑68 (MQ=255)
                               tCGTACAGGGATTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACcaacg                               >  1:1562913/1‑68 (MQ=255)
                               tCGTACAGGGATTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACcaacg                               >  1:575239/1‑68 (MQ=255)
                               tCGTACAGGGATTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACcaacg                               >  1:1234488/1‑68 (MQ=255)
                                cGTACAGGGATTTACCCACATCGTGGCCTTGtgctgc                                                              <  1:2685258/37‑1 (MQ=255)
                                         aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                     <  1:393127/69‑1 (MQ=255)
                                         aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                     <  1:189097/69‑1 (MQ=255)
                                         aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                     <  1:777629/69‑1 (MQ=255)
                                         aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                     <  1:623079/69‑1 (MQ=255)
                                         aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                     <  1:2785346/69‑1 (MQ=255)
                                         aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                     <  1:2765651/69‑1 (MQ=255)
                                         aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                     <  1:2709144/69‑1 (MQ=255)
                                         aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                     <  1:1043693/69‑1 (MQ=255)
                                         aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                     <  1:874896/69‑1 (MQ=255)
                                         aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                     <  1:1735814/69‑1 (MQ=255)
                                         aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                     <  1:437334/69‑1 (MQ=255)
                                         aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                     <  1:904296/69‑1 (MQ=255)
                                         aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                     <  1:2080666/69‑1 (MQ=255)
                                         aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                     <  1:548997/69‑1 (MQ=255)
                                         aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                     <  1:99090/69‑1 (MQ=255)
                                         aTTTACCCACATCGTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                     <  1:1145789/69‑1 (MQ=255)
                                            tACCCACATCGTGGCCTTGTGCCGCGATAAAGGTGTTAGCGATACCACCACCAACAATCAGCt                        >  1:197121/1‑63 (MQ=255)
                                            tACCCACATCGTGGCCTTGTGCCGCGATAAAGGTGTTAGCGATACCACCACCAACAATCAGCTGGTCa                   >  1:1489071/1‑68 (MQ=255)
                                            tACCCACATCGTGGCCTTGTGCCGCGATAAAGGTGTTAGCGATACCACCACCAACAATCAGCTGGTCa                   >  1:605161/1‑68 (MQ=255)
                                            tACCCACATCGTGGCCTTGTGCCGCGATAAAGGTGTTAGCGATACCACCACCAACAATCAGCTGGTCa                   >  1:3058186/1‑68 (MQ=255)
                                            tACCCACATCGTGGCCTTGTGCCGCGATAAAGGTGTTAGCGATACCACCACCAACAATCAGCTGGTCa                   >  1:2961781/1‑68 (MQ=255)
                                            tACCCACATCGTGGCCTTGTGCCGCGATAAAGGTGTTAGCGATACCACCACCAACAATCAGCTGGTCa                   >  1:2956146/1‑68 (MQ=255)
                                            tACCCACATCGTGGCCTTGTGCCGCGATAAAGGTGTTAGCGATACCACCACCAACAATCAGCTGGTCa                   >  1:267273/1‑68 (MQ=255)
                                            tACCCACATCGTGGCCTTGTGCCGCGATAAAGGTGTTAGCGATACCACCACCAACAATCAGCTGGTCa                   >  1:2474848/1‑68 (MQ=255)
                                            tACCCACATCGTGGCCTTGTGCCGCGATAAAGGTGTTAGCGATACCACCACCAACAATCAGCTGGTCa                   >  1:1813248/1‑68 (MQ=255)
                                            tACCCACATCGTGGCCTTGTGACGCGATAAAGGTGTTAGCGATACCACCACCAACAATCAGCTGGt                     >  1:1925618/1‑66 (MQ=255)
                                                    tCGTGGCCTTGTGCCGCGATAAAGGTGTTAGCGATACCACCACCAACAATCAGCTGGTCAGCGATTTTa          <  1:2709575/69‑1 (MQ=255)
                                                    tCGTGGCCTTGTGCCGCGATAAAGGTGTTAGCGATACCACCACCAACAATCAGCTGGTCAGCGATTTTa          <  1:908313/69‑1 (MQ=255)
                                                      gTGGCCTTGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGt                     <  1:1702365/56‑1 (MQ=255)
                                                            ttGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGTCAGCGATTTTAGACAggg   >  1:285083/1‑68 (MQ=255)
                                                            ttGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGTCAGCGATTTTAGACAGGGa  >  1:1777995/1‑69 (MQ=255)
                                                            ttGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGTCAGCGATTTTAGACAGGGa  >  1:1424405/1‑69 (MQ=255)
                                                            ttGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGTCAGCGATTTTAGACAGGGa  >  1:3052192/1‑69 (MQ=255)
                                                            ttGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGTCAGCGATTTTAGACAGGGa  >  1:2975565/1‑69 (MQ=255)
                                                            ttGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGTCAGCGATTTTAGACAGGGa  >  1:2529121/1‑69 (MQ=255)
                                                            ttGTGCTGCGATAAAGGTGTTAGCAATACCACCACCAACGATCAGCTGGTCAGCGATTTTAGACAGGGa  >  1:1995758/1‑69 (MQ=255)
                                                              gtgCTGCGATAAAGGTGTTAGCAATACCACCACcaacg                               >  1:578727/1‑37 (MQ=25)
                                                              gtgCTGCGATAAAGGTGTTAGCAATACCACCACcaacg                               >  1:637433/1‑37 (MQ=25)
                                                              gtgCTGCGATAAAGGTGTTAGCAATACCACCACcaacg                               >  1:3074893/1‑37 (MQ=25)
                                                              gtgCTGCGATAAAGGTGTTAGCAATACCACCACcaacg                               >  1:1122089/1‑37 (MQ=25)
                                                              gtgCTGCGATAAAGGTGTTAGCAATACCACCACcaacg                               >  1:1568256/1‑37 (MQ=25)
                                                              gtgCTGCGATAAAGGTGTTAGCAATACCACCACcaacg                               >  1:2036803/1‑37 (MQ=25)
                                                              gtgCTGCGATAAAGGTGTTAGCAATACCACCACcaacg                               >  1:109126/1‑37 (MQ=25)
                                                                  |                                                              
CAGACGTTTAGCTTCGTCAACCAGGTCAGCTTCGTACAGGGATTTACCCACATCGTGGCCTTGTGCCGCGATAAAGGTGTTAGCGATACCACCACCAACAATCAGCTGGTCAGCGATTTTAGACAGGGA  >  minE/1960714‑1960842

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A