BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819118.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,083,117 number of mapped reads = 993,995 (91.77%) number of supplementary alignments = 3,936 (0.36%) number of secondary alignments = 0 number of mapped bases = 57,865,048 bp number of sequenced bases = 57,846,881 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 28,353 duplication rate = 2.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8613 >>>>>>> ACTG content number of A's = 13,764,509 bp (23.79%) number of C's = 10,888,999 bp (18.82%) number of T's = 18,540,884 bp (32.05%) number of G's = 14,651,707 bp (25.33%) number of N's = 782 bp (0%) GC percentage = 44.15% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 293,854 number of insertions = 3,157 mapped reads with insertion percentage = 0.32% number of deletions = 10,823 mapped reads with deletion percentage = 1.08% homopolymer indels = 43.81% >>>>>>> Coverage mean coverageData = 0.0187X std coverageData = 0.1879X There is a 1.72% of reference with a coverageData >= 1X There is a 0.1% 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 5730648 0.022991509417342636 0.3058178468985606 chr2 243199373 4588691 0.01886802150596005 0.21071178213843303 chr3 198022430 3154493 0.01592997823529385 0.13467545944071152 chr4 191154276 3243418 0.016967540919670558 0.14949794487390672 chr5 180915260 3166107 0.017500497194100708 0.1406510143954756 chr6 171115067 2477493 0.014478520468334912 0.15132072080890333 chr7 159138663 2903397 0.01824444761107488 0.2305932827034713 chr8 146364022 5245629 0.035839606812663294 0.22514997242518786 chr9 141213431 2465830 0.017461724302980784 0.17025194952499983 chr10 135534747 3024159 0.022312794814159355 0.19775943411024485 chr11 135006516 2002149 0.014830017537820175 0.1700821074616633 chr12 133851895 2697644 0.02015394701733584 0.15050264516762338 chr13 115169878 1271348 0.011038893346748183 0.11157349900248595 chr14 107349540 1359148 0.012660957839223158 0.12125883257511309 chr15 102531392 1534303 0.014964226760912405 0.13209204739805494 chr16 90354753 1794333 0.01985875607451442 0.156987144315412 chr17 81195210 2045641 0.025194109356943592 0.17462508371112662 chr18 78077248 1369011 0.017534058065161312 0.2750498799066379 chr19 59128983 1201669 0.020322842352962507 0.24294947525724095 chr20 63025520 1662066 0.0263713175234413 0.17459979490722083 chr21 48129895 793540 0.01648746584633106 0.14421988989258488 chr22 51304566 482513 0.009404874412152712 0.10246212276326723 chrMT 16571 4674 0.28205901876772677 0.5634908559502843 chrX 155270560 3454064 0.02224545335574239 0.1716124116986253 chrY 59373566 193080 0.0032519522239913973 0.09831314765371292