BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081178.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,021,456 number of mapped reads = 1,832,984 (90.68%) number of supplementary alignments = 18,672 (0.92%) number of secondary alignments = 0 number of mapped bases = 123,393,038 bp number of sequenced bases = 123,348,611 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 73,245 duplication rate = 3.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1456 >>>>>>> ACTG content number of A's = 35,018,744 bp (28.39%) number of C's = 22,547,710 bp (18.28%) number of T's = 39,261,974 bp (31.83%) number of G's = 26,483,672 bp (21.47%) number of N's = 36,511 bp (0.03%) GC percentage = 39.75% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 993,084 number of insertions = 9,785 mapped reads with insertion percentage = 0.53% number of deletions = 27,676 mapped reads with deletion percentage = 1.5% homopolymer indels = 47.44% >>>>>>> Coverage mean coverageData = 0.0399X std coverageData = 0.3185X There is a 3.46% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 8898110 0.035699449671581764 0.53826496749325 chr2 243199373 10821639 0.04449698560694891 0.3808292039931604 chr3 198022430 8710203 0.043985941390578834 0.23410443784509108 chr4 191154276 8576818 0.04486856469797202 0.24442575500451078 chr5 180915260 7824384 0.04324888901024712 0.23398400460808852 chr6 171115067 7448948 0.04353180658252613 0.2830146303921933 chr7 159138663 6661651 0.04186066964757647 0.2902183995219157 chr8 146364022 7275532 0.04970847275568855 0.4826873876669325 chr9 141213431 5889045 0.041703150743501165 0.31078262210189106 chr10 135534747 5778204 0.04263263943673426 0.28012496241562107 chr11 135006516 5405233 0.04003683051860993 0.29970749646315736 chr12 133851895 5872157 0.04387055558682976 0.23779962990783174 chr13 115169878 4063377 0.03528159507123903 0.20961355846412025 chr14 107349540 3670154 0.034188819067133405 0.2209943932865891 chr15 102531392 3320408 0.03238430626202753 0.20409721114453322 chr16 90354753 2665947 0.029505332165536437 0.2111555713117698 chr17 81195210 2940702 0.03621767835811989 0.23370303913209572 chr18 78077248 3206493 0.041068212342730115 0.5118417726521401 chr19 59128983 2011826 0.03402436331434958 0.36903977443641217 chr20 63025520 2261235 0.035878085575493865 0.22084579300232446 chr21 48129895 2046263 0.04251542622314052 0.24336099353600876 chr22 51304566 1155711 0.02252647454419554 0.1659480104668278 chrMT 16571 4534 0.2736105244101141 0.5984838871247428 chrX 155270560 6592235 0.04245643861914326 0.24742386573919414 chrY 59373566 292229 0.004921870449890108 0.10377332702480521