BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238628.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 = 2,279,071 number of mapped reads = 1,365,065 (59.9%) number of supplementary alignments = 12,720 (0.56%) number of secondary alignments = 0 number of mapped bases = 81,263,508 bp number of sequenced bases = 81,224,732 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 614,379 duplication rate = 24.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.5176 >>>>>>> ACTG content number of A's = 19,445,785 bp (23.94%) number of C's = 13,545,698 bp (16.68%) number of T's = 28,388,877 bp (34.95%) number of G's = 19,842,665 bp (24.43%) number of N's = 1,707 bp (0%) GC percentage = 41.11% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 516,082 number of insertions = 6,223 mapped reads with insertion percentage = 0.45% number of deletions = 23,017 mapped reads with deletion percentage = 1.67% homopolymer indels = 39.34% >>>>>>> Coverage mean coverageData = 0.0263X std coverageData = 0.62X There is a 0.77% of reference with a coverageData >= 1X There is a 0.42% of reference with a coverageData >= 2X There is a 0.31% of reference with a coverageData >= 3X There is a 0.24% of reference with a coverageData >= 4X There is a 0.18% of reference with a coverageData >= 5X There is a 0.14% of reference with a coverageData >= 6X There is a 0.11% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% 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 4255279 0.017072290463821953 0.3533599251943122 chr2 243199373 7617786 0.03132321397884525 1.2430917397846333 chr3 198022430 3377213 0.017054699308558127 0.351724074375801 chr4 191154276 2666931 0.013951720337137527 0.32800635563588215 chr5 180915260 2272539 0.012561345018656802 0.2989441216878695 chr6 171115067 13594402 0.0794459671982012 0.8830199484587434 chr7 159138663 4001166 0.02514263928433281 0.48701922379637325 chr8 146364022 2208608 0.015089828564563496 0.3906237043864383 chr9 141213431 10359525 0.0733607626883593 0.8324991945000365 chr10 135534747 2574332 0.018993889441502407 0.4412105146383379 chr11 135006516 2363393 0.017505769869655772 0.37350251304692134 chr12 133851895 1894277 0.01415203721994373 0.4002966221574757 chr13 115169878 1955164 0.016976348624768014 0.4414631474718225 chr14 107349540 5967246 0.055587066325575314 0.7056955241323073 chr15 102531392 1520558 0.014830170256539578 0.38676209548435536 chr16 90354753 2918742 0.03230313739001644 0.5422061167527977 chr17 81195210 882228 0.010865517805791746 0.27642664497582103 chr18 78077248 4119260 0.052758775514218946 1.4803354174914756 chr19 59128983 695837 0.011768120550965674 0.3371333965702512 chr20 63025520 2212414 0.03510346285123867 0.5403463082762507 chr21 48129895 1122929 0.023331216492369244 0.45848405517754365 chr22 51304566 286279 0.005579990677632864 0.1816445078927325 chrMT 16571 345874 20.87224669603524 16.716143216652114 chrX 155270560 1757639 0.011319847110746557 0.30899051321452004 chrY 59373566 293887 0.004949795334846487 0.2540753674462328