BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173888.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 2,278,166 number of mapped reads = 2,219,075 (97.41%) number of supplementary alignments = 225,955 (9.92%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,111,746 number of mapped paired reads (second in pair) = 1,107,329 number of mapped paired reads (both in pair) = 2,179,914 number of mapped paired reads (singletons) = 39,161 number of mapped bases = 262,990,080 bp number of sequenced bases = 262,834,614 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,780,570 duplication rate = 65.41% >>>>>>> Insert size mean insert size = 1,189,302.7518 std insert size = 9,974,636.1795 median insert size = 209 >>>>>>> Mapping quality mean mapping quality = 52.8316 >>>>>>> ACTG content number of A's = 79,355,871 bp (30.19%) number of C's = 51,201,877 bp (19.48%) number of T's = 79,186,381 bp (30.13%) number of G's = 53,087,536 bp (20.2%) number of N's = 2,949 bp (0%) GC percentage = 39.68% >>>>>>> Mismatches and indels general error rate = 0.0112 number of mismatches = 2,852,693 number of insertions = 30,020 mapped reads with insertion percentage = 1.31% number of deletions = 61,433 mapped reads with deletion percentage = 2.7% homopolymer indels = 43.39% >>>>>>> Coverage mean coverageData = 0.085X std coverageData = 1.3852X There is a 1.66% of reference with a coverageData >= 1X There is a 1.32% of reference with a coverageData >= 2X There is a 1.05% of reference with a coverageData >= 3X There is a 0.88% of reference with a coverageData >= 4X There is a 0.7% of reference with a coverageData >= 5X There is a 0.57% of reference with a coverageData >= 6X There is a 0.44% of reference with a coverageData >= 7X There is a 0.36% of reference with a coverageData >= 8X There is a 0.27% of reference with a coverageData >= 9X There is a 0.22% of reference with a coverageData >= 10X There is a 0.16% of reference with a coverageData >= 11X There is a 0.14% of reference with a coverageData >= 12X There is a 0.11% of reference with a coverageData >= 13X There is a 0.09% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% 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 21021897 0.08434039969753977 1.1003177395454327 chr2 243199373 23824447 0.09796261686908214 3.5804694228743568 chr3 198022430 18024669 0.09102337043333929 0.9096858942857468 chr4 191154276 18252049 0.09548334142418033 1.1239820902605704 chr5 180915260 16544788 0.0914504835026078 0.9151182941771216 chr6 171115067 15161622 0.08860483337799821 0.9398128809685022 chr7 159138663 15058006 0.0946219210098554 1.1214346002282687 chr8 146364022 13522876 0.09239207706385658 1.2296763357515414 chr9 141213431 11093253 0.07855664239189826 1.1091380459425564 chr10 135534747 13178738 0.0972351245101745 1.2304224046772492 chr11 135006516 12312604 0.0912000721505916 0.9165130083298968 chr12 133851895 11724839 0.08759561454098203 0.8859576403266322 chr13 115169878 9321767 0.08093927997388345 0.8602431860647779 chr14 107349540 8571994 0.07985124109521102 0.8490995189812051 chr15 102531392 7471203 0.07286746872606586 0.8151538277816981 chr16 90354753 7834341 0.08670646247021449 1.0016532649320944 chr17 81195210 6895870 0.08492951739394479 0.8913573559145384 chr18 78077248 7180563 0.09196741924100603 1.2777277259925133 chr19 59128983 4552656 0.07699533746420094 0.9453226373082197 chr20 63025520 5461079 0.08664869405282177 0.9034411414896987 chr21 48129895 3805790 0.07907330776433233 0.9951934387012026 chr22 51304566 2939278 0.057290768232987295 0.7394357876915076 chrMT 16571 251213 15.159797236135418 15.69699141858953 chrX 155270560 6899744 0.04443691064165673 0.6314374351448763 chrY 59373566 2084794 0.03511316803844997 0.7102289034094762