BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084865.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,051,527 number of mapped reads = 1,857,220 (90.53%) number of supplementary alignments = 20,665 (1.01%) number of secondary alignments = 0 number of mapped bases = 124,427,751 bp number of sequenced bases = 124,381,070 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 83,372 duplication rate = 3.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5234 >>>>>>> ACTG content number of A's = 33,901,429 bp (27.26%) number of C's = 23,456,330 bp (18.86%) number of T's = 38,865,003 bp (31.25%) number of G's = 28,141,084 bp (22.62%) number of N's = 17,224 bp (0.01%) GC percentage = 41.48% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 950,601 number of insertions = 9,718 mapped reads with insertion percentage = 0.52% number of deletions = 28,523 mapped reads with deletion percentage = 1.52% homopolymer indels = 48.27% >>>>>>> Coverage mean coverageData = 0.0402X std coverageData = 0.2808X There is a 3.35% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.1% 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% 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 9904449 0.0397369080175732 0.3307683309010054 chr2 243199373 10356094 0.04258273313887203 0.45052705224564055 chr3 198022430 10661429 0.05383950191905028 0.2712644898048672 chr4 191154276 7201506 0.037673789729924745 0.2282457941951429 chr5 180915260 6608314 0.03652712325096291 0.22385520155314975 chr6 171115067 7673979 0.04484689241304508 0.2636455442242703 chr7 159138663 7595325 0.0477277165511941 0.2862145025596687 chr8 146364022 6634471 0.045328564420018466 0.28856274797645876 chr9 141213431 8457289 0.05989011767584629 0.33080837051715783 chr10 135534747 4110889 0.030330886292944496 0.2100828144909792 chr11 135006516 5488331 0.04065234155068486 0.2682064424557733 chr12 133851895 5623152 0.04201025319813365 0.2417065630376544 chr13 115169878 3076980 0.02671688164851577 0.19112194648058495 chr14 107349540 2714601 0.025287495409854574 0.19245991935197657 chr15 102531392 2988193 0.02914417664396871 0.20673460234537142 chr16 90354753 2599887 0.028774214013954528 0.2046030455244349 chr17 81195210 2838921 0.03496414382079928 0.2268256503309416 chr18 78077248 4040126 0.05174524081586482 0.4070889836157471 chr19 59128983 2533377 0.04284492767277935 0.28330342375129786 chr20 63025520 2435539 0.038643695442734945 0.23121537115214416 chr21 48129895 1003944 0.02085905236236231 0.17370058659140375 chr22 51304566 1096499 0.021372347248780937 0.168885309697397 chrMT 16571 24611 1.4851849616800434 1.565865180361055 chrX 155270560 8469120 0.05454427420111063 0.27989567117267666 chrY 59373566 290725 0.0048965393117873365 0.10884720029184283