BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524425.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 2,162,552 number of mapped reads = 1,982,397 (91.67%) number of supplementary alignments = 8,092 (0.37%) number of secondary alignments = 0 number of mapped bases = 117,815,597 bp number of sequenced bases = 117,782,974 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 107,952 duplication rate = 4.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2577 >>>>>>> ACTG content number of A's = 29,096,222 bp (24.7%) number of C's = 23,149,276 bp (19.65%) number of T's = 34,853,188 bp (29.59%) number of G's = 30,671,988 bp (26.04%) number of N's = 12,300 bp (0.01%) GC percentage = 45.7% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 600,673 number of insertions = 7,148 mapped reads with insertion percentage = 0.36% number of deletions = 20,441 mapped reads with deletion percentage = 1.02% homopolymer indels = 43.87% >>>>>>> Coverage mean coverageData = 0.0381X std coverageData = 0.3656X There is a 3.24% of reference with a coverageData >= 1X There is a 0.4% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 9880175 0.03963952009571924 0.7764217599837336 chr2 243199373 9386932 0.03859768174649036 0.4108585755037296 chr3 198022430 7838926 0.03958605093372503 0.22527994489703682 chr4 191154276 7719915 0.04038578242424459 0.2975843020907111 chr5 180915260 7253198 0.040091687124679254 0.22734345223088054 chr6 171115067 4428905 0.02588261266320867 0.1962184525116362 chr7 159138663 6848773 0.04303651212653458 0.48852546244209333 chr8 146364022 6003631 0.04101848881960896 0.28234876353404165 chr9 141213431 4254757 0.03012997396826935 0.24211881818000533 chr10 135534747 5979285 0.04411625160594427 0.4036996732738857 chr11 135006516 4933037 0.03653925118695753 0.2712700252875566 chr12 133851895 5414271 0.04044971496294468 0.23546922578816354 chr13 115169878 3755188 0.032605643638868836 0.20558264973795273 chr14 107349540 3105961 0.028933156117855744 0.1989983158793869 chr15 102531392 3554207 0.034664573753177955 0.21352319457498964 chr16 90354753 3709662 0.04105663373347941 0.24705365098681098 chr17 81195210 3202930 0.03944727773965977 0.25422552419947153 chr18 78077248 3164007 0.040524058942241405 0.4668439859565724 chr19 59128983 3863766 0.06534470582725903 0.527558567877478 chr20 63025520 3725930 0.059117798631411526 0.30023339339841215 chr21 48129895 1622690 0.03371480448897717 0.2594574819829393 chr22 51304566 828190 0.01614261779351179 0.1447394411976427 chrMT 16571 13545 0.8173918290990284 1.1223521184840612 chrX 155270560 6907889 0.044489367462833905 0.26097852524792287 chrY 59373566 419827 0.007070941300712846 0.2372191603295589