BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716968.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 = 1,019,244 number of mapped reads = 809,905 (79.46%) number of supplementary alignments = 2,470 (0.24%) number of secondary alignments = 0 number of mapped bases = 44,409,571 bp number of sequenced bases = 44,397,925 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,497 duplication rate = 1.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.4381 >>>>>>> ACTG content number of A's = 10,079,744 bp (22.7%) number of C's = 9,622,762 bp (21.67%) number of T's = 13,006,806 bp (29.3%) number of G's = 11,687,358 bp (26.32%) number of N's = 1,255 bp (0%) GC percentage = 48% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 231,320 number of insertions = 3,216 mapped reads with insertion percentage = 0.39% number of deletions = 6,992 mapped reads with deletion percentage = 0.86% homopolymer indels = 33.74% >>>>>>> Coverage mean coverageData = 0.0143X std coverageData = 0.1399X There is a 1.32% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 4395440 0.017634620055771096 0.1687420449260502 chr2 243199373 3862324 0.01588130739136404 0.16063670256912393 chr3 198022430 2992366 0.015111247751075472 0.13273351694241015 chr4 191154276 2830516 0.014807495072723354 0.1385426395174103 chr5 180915260 2704278 0.014947760625610023 0.13035209001951795 chr6 171115067 1903036 0.01112138184768966 0.1146963314544867 chr7 159138663 2527801 0.015884266917587462 0.15523846379993644 chr8 146364022 2721542 0.018594337343367073 0.15159125718799474 chr9 141213431 1924589 0.01362893732112493 0.13058573278300842 chr10 135534747 2295480 0.016936468697580555 0.17757726791742007 chr11 135006516 1817083 0.013459224442174332 0.13994203288073162 chr12 133851895 2156819 0.016113473776370516 0.13628616521723366 chr13 115169878 807481 0.007011216943374725 0.0917390653538132 chr14 107349540 1427714 0.013299675061486058 0.12514745305310157 chr15 102531392 897946 0.008757766596985243 0.10099890046279712 chr16 90354753 1230251 0.013615786211047469 0.1322532775272156 chr17 81195210 1798758 0.022153498956403957 0.16512790613839712 chr18 78077248 1183084 0.015152736940728238 0.1525918201598142 chr19 59128983 1208077 0.020431215602000122 0.16560605153019575 chr20 63025520 1147091 0.018200421035796294 0.1513893323878144 chr21 48129895 603418 0.012537280623612413 0.12702255956067474 chr22 51304566 492282 0.009595286314282437 0.10528696303434432 chrMT 16571 11618 0.7011043389053165 1.050788359475465 chrX 155270560 1347535 0.008678625233270235 0.10476140700112004 chrY 59373566 123042 0.0020723363659848225 0.06690975070470105