BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238261.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 1,562,948 number of mapped reads = 1,393,418 (89.15%) number of supplementary alignments = 11,201 (0.72%) number of secondary alignments = 0 number of mapped bases = 90,534,962 bp number of sequenced bases = 90,491,533 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 39,970 duplication rate = 1.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.817 >>>>>>> ACTG content number of A's = 25,214,010 bp (27.86%) number of C's = 17,371,512 bp (19.2%) number of T's = 27,092,008 bp (29.94%) number of G's = 20,795,522 bp (22.98%) number of N's = 18,481 bp (0.02%) GC percentage = 42.18% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 797,925 number of insertions = 7,926 mapped reads with insertion percentage = 0.56% number of deletions = 25,893 mapped reads with deletion percentage = 1.84% homopolymer indels = 44.18% >>>>>>> Coverage mean coverageData = 0.0292X std coverageData = 0.3072X There is a 2.65% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 7759094 0.031129687737066862 0.5296226956282312 chr2 243199373 6443048 0.026492864354547493 0.34562721593652534 chr3 198022430 6395402 0.03229635147897135 0.19318955871311697 chr4 191154276 5069141 0.026518585438287553 0.20171523134229138 chr5 180915260 6721109 0.03715059194011605 0.2093864280285106 chr6 171115067 4710802 0.02753002457697077 0.20425780618449357 chr7 159138663 5693415 0.03577644107767827 0.44008784366026754 chr8 146364022 4496040 0.030718204778493994 0.4318494743588811 chr9 141213431 4301463 0.030460721544255942 0.29259528869870677 chr10 135534747 4601032 0.03394725044198445 0.34334449613893414 chr11 135006516 3747260 0.02775614178503799 0.22820319797167896 chr12 133851895 4132933 0.030876910633203962 0.19239134525632648 chr13 115169878 3105853 0.02696758088082719 0.17520355161189854 chr14 107349540 2196135 0.020457796093024713 0.19574283464161005 chr15 102531392 2534248 0.024716800879871017 0.17006393440502313 chr16 90354753 2540598 0.028118033812786804 0.2144590366773484 chr17 81195210 2386095 0.0293871399556698 0.2026251517440587 chr18 78077248 2260586 0.028953197735657896 0.530119437065102 chr19 59128983 1902681 0.032178483435103225 0.41869502756057303 chr20 63025520 1876463 0.029773066529240853 0.19542278178458564 chr21 48129895 1166798 0.024242687419118617 0.19352383609785775 chr22 51304566 971706 0.018939951660442853 0.14733634942267648 chrMT 16571 4387 0.2647396053346207 0.5526225901125205 chrX 155270560 5212468 0.03357022735024592 0.21969790221307667 chrY 59373566 306205 0.005157261398111072 0.15210732654283915