BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237265.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 = 2,715,753 number of mapped reads = 2,126,652 (78.31%) number of supplementary alignments = 12,793 (0.47%) number of secondary alignments = 0 number of mapped bases = 139,813,829 bp number of sequenced bases = 139,730,759 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 115,884 duplication rate = 4.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9173 >>>>>>> ACTG content number of A's = 38,810,792 bp (27.78%) number of C's = 25,302,614 bp (18.11%) number of T's = 44,669,165 bp (31.97%) number of G's = 30,946,124 bp (22.15%) number of N's = 2,064 bp (0%) GC percentage = 40.26% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,136,661 number of insertions = 9,946 mapped reads with insertion percentage = 0.46% number of deletions = 47,557 mapped reads with deletion percentage = 2.2% homopolymer indels = 45.14% >>>>>>> Coverage mean coverageData = 0.0452X std coverageData = 0.4116X There is a 3.58% of reference with a coverageData >= 1X There is a 0.66% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 17987872 0.07216781217166958 0.8491788558072217 chr2 243199373 11721259 0.04819609053844066 0.4286703013302425 chr3 198022430 8200694 0.04141295508796655 0.2585990661689856 chr4 191154276 2728701 0.014274862467633211 0.19373729861465033 chr5 180915260 9718683 0.05371953145356561 0.2859770789550047 chr6 171115067 7390528 0.04319039889105732 0.27014887536003135 chr7 159138663 9112073 0.05725870023175952 0.5076883676532727 chr8 146364022 6975742 0.04766022349399499 0.4178506768839894 chr9 141213431 6980095 0.04942939882255251 0.3929022272275184 chr10 135534747 5791721 0.042732370319767524 0.505269483201675 chr11 135006516 7443009 0.05513073902299649 0.3696616589769725 chr12 133851895 5761134 0.04304110898093748 0.2585034998926666 chr13 115169878 2122375 0.018428212626916216 0.16004656972209172 chr14 107349540 5296462 0.04933846945222122 0.29254898393465417 chr15 102531392 4555080 0.04442619875871772 0.2557617175207775 chr16 90354753 1553054 0.017188404023416454 0.20301337733018435 chr17 81195210 4132532 0.050896253609049105 0.32346774711815124 chr18 78077248 3210016 0.041113334322439236 0.5789209343548842 chr19 59128983 2486876 0.04205849439351934 0.474279420923114 chr20 63025520 1270310 0.020155486222089083 0.18343810368675081 chr21 48129895 3925122 0.08155268155062462 0.37933429985361977 chr22 51304566 229814 0.004479406374863399 0.0760646395227408 chrMT 16571 92103 5.558083398708587 3.9285598093299345 chrX 155270560 10773564 0.0693857483350353 0.3468007236121037 chrY 59373566 355010 0.005979260198048404 0.16541298518107794