BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2971320.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 93,057,651 number of mapped reads = 72,420,823 (77.82%) number of secondary alignments = 0 number of mapped bases = 2,860,780,206 bp number of sequenced bases = 2,860,496,233 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,078,470 duplication rate = 11.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.4311 >>>>>>> ACTG content number of A's = 818,613,323 bp (28.62%) number of C's = 602,731,304 bp (21.07%) number of T's = 827,294,799 bp (28.92%) number of G's = 611,709,835 bp (21.38%) number of N's = 146,972 bp (0.01%) GC percentage = 42.46% >>>>>>> Mismatches and indels general error rate = 0.0032 number of mismatches = 9,033,593 number of insertions = 104,678 mapped reads with insertion percentage = 0.14% number of deletions = 222,899 mapped reads with deletion percentage = 0.31% homopolymer indels = 39.76% >>>>>>> Coverage mean coverageData = 0.9241X std coverageData = 6.6047X There is a 34.23% of reference with a coverageData >= 1X There is a 20.13% of reference with a coverageData >= 2X There is a 12.27% of reference with a coverageData >= 3X There is a 7.67% of reference with a coverageData >= 4X There is a 4.92% of reference with a coverageData >= 5X There is a 3.24% of reference with a coverageData >= 6X There is a 2.18% of reference with a coverageData >= 7X There is a 1.5% of reference with a coverageData >= 8X There is a 1.06% of reference with a coverageData >= 9X There is a 0.76% of reference with a coverageData >= 10X There is a 0.55% of reference with a coverageData >= 11X There is a 0.41% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.23% of reference with a coverageData >= 14X There is a 0.18% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.11% of reference with a coverageData >= 17X There is a 0.09% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 224312114 0.8999460587101206 8.940885421576453 chr2 243199373 243032256 0.9993128395113091 7.059416153193552 chr3 198022430 194152708 0.9804581632494864 2.193471719803377 chr4 191154276 184234745 0.9638013276773364 2.296932086461132 chr5 180915260 178069478 0.984270083131738 2.432174164775466 chr6 171115067 168515262 0.9848066856672534 3.4959836635492083 chr7 159138663 161114449 1.0124154995571377 13.280104457711788 chr8 146364022 146332297 0.9997832459127148 5.499660721187447 chr9 141213431 120971273 0.8566555754884251 7.578649690123586 chr10 135534747 130575679 0.9634110948685358 3.8395757300949516 chr11 135006516 132919234 0.984539398083571 11.497732784154925 chr12 133851895 129787757 0.9696370529531912 2.7163004060992084 chr13 115169878 91819338 0.7972513264275577 1.825339645145604 chr14 107349540 87839780 0.8182594913774199 5.180179414160939 chr15 102531392 82155958 0.801276139896745 2.0014888807848012 chr16 90354753 78141855 0.8648339174807993 3.5800371920343492 chr17 81195210 72158132 0.8886993703199979 3.879508129349395 chr18 78077248 77185022 0.9885725224331677 15.64984309503848 chr19 59128983 53195122 0.8996454750456303 9.924843986492244 chr20 63025520 58132868 0.922370303331095 2.4578684960652444 chr21 48129895 36089379 0.7498329053076056 3.257334932441312 chr22 51304566 29659139 0.5780994034721978 3.0632332635280672 chrMT 16571 287432 17.34548307283809 18.162558059432076 chrX 155270560 171237669 1.1028341045462835 4.999070160182528 chrY 59373566 8861260 0.14924587820782062 1.3479229961150414