BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013239.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 = 1,220,771 number of mapped reads = 591,267 (48.43%) number of supplementary alignments = 7,304 (0.6%) number of secondary alignments = 0 number of mapped bases = 37,804,960 bp number of sequenced bases = 37,777,901 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 34,971 duplication rate = 5.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6155 >>>>>>> ACTG content number of A's = 10,429,854 bp (27.61%) number of C's = 6,802,198 bp (18.01%) number of T's = 12,186,093 bp (32.26%) number of G's = 8,350,969 bp (22.11%) number of N's = 8,787 bp (0.02%) GC percentage = 40.11% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 340,177 number of insertions = 2,682 mapped reads with insertion percentage = 0.45% number of deletions = 15,570 mapped reads with deletion percentage = 2.58% homopolymer indels = 43.39% >>>>>>> Coverage mean coverageData = 0.0122X std coverageData = 0.1547X There is a 0.95% of reference with a coverageData >= 1X There is a 0.2% of reference with a coverageData >= 2X There is a 0.05% 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 2871614 0.01152099035291872 0.18151991194532976 chr2 243199373 3493694 0.014365555128302078 0.19214117573016656 chr3 198022430 3738474 0.01887904314677888 0.17338748793503608 chr4 191154276 2113186 0.011054871720473572 0.1311137166488814 chr5 180915260 1515938 0.00837927104656622 0.11100206917174028 chr6 171115067 1598974 0.009344437214286922 0.12861740718046344 chr7 159138663 2285386 0.014360972732314585 0.19129478187594118 chr8 146364022 2486630 0.016989352752276785 0.19929047532409408 chr9 141213431 850981 0.006026204405443558 0.1029903430901634 chr10 135534747 2803142 0.020682091213111573 0.19879497632807105 chr11 135006516 1908843 0.014138895340429346 0.15530120069258 chr12 133851895 1668978 0.012468841027614887 0.1421658444084951 chr13 115169878 922949 0.008013805484798724 0.1113213111493989 chr14 107349540 1046485 0.009748388302362543 0.1214041514565197 chr15 102531392 655289 0.006391106052671167 0.0979129583285153 chr16 90354753 865320 0.009576917331620617 0.12214882590404584 chr17 81195210 732313 0.0090191650468051 0.11886598334123552 chr18 78077248 869862 0.011141043290870088 0.16254143806480284 chr19 59128983 548527 0.009276787324415845 0.15042679368143957 chr20 63025520 634983 0.01007501405779754 0.12643333451067856 chr21 48129895 622476 0.012933250737405515 0.14466253474762047 chr22 51304566 158988 0.0030989054658409937 0.06722635153706807 chrMT 16571 14463 0.8727898135296602 1.241817449951666 chrX 155270560 3281743 0.02113564219772248 0.19083212818397782 chrY 59373566 115722 0.0019490491778782497 0.061912698399164995