BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708622.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 3,311,902 number of mapped reads = 2,401,878 (72.52%) number of supplementary alignments = 786 (0.02%) number of secondary alignments = 0 number of mapped bases = 116,936,374 bp number of sequenced bases = 116,913,835 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 88,889 duplication rate = 2.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1296 >>>>>>> ACTG content number of A's = 34,529,947 bp (29.53%) number of C's = 21,962,607 bp (18.79%) number of T's = 36,913,698 bp (31.57%) number of G's = 23,497,428 bp (20.1%) number of N's = 10,155 bp (0.01%) GC percentage = 38.88% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 746,339 number of insertions = 5,497 mapped reads with insertion percentage = 0.23% number of deletions = 14,649 mapped reads with deletion percentage = 0.61% homopolymer indels = 48.33% >>>>>>> Coverage mean coverageData = 0.0378X std coverageData = 0.3988X There is a 3.2% of reference with a coverageData >= 1X There is a 0.42% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.01% 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 9123848 0.03660511642215728 0.7464145627239517 chr2 243199373 10108596 0.04156505781780943 0.4095602048401497 chr3 198022430 8022940 0.04051530930107261 0.23191899985382286 chr4 191154276 8098530 0.04236646006286566 0.24049138388852973 chr5 180915260 7464911 0.04126192008346891 0.23568730758963832 chr6 171115067 7162850 0.04185984393764694 0.3175611171327632 chr7 159138663 6686745 0.042018356029546386 0.5523909948262609 chr8 146364022 6145116 0.041985153974519775 0.745326069872248 chr9 141213431 4885912 0.03459948508722233 0.302303126253601 chr10 135534747 5485925 0.040476151846138765 0.3111215780382108 chr11 135006516 5280952 0.03911627495075867 0.30279973952620787 chr12 133851895 5376111 0.04016462374327984 0.2388514319872322 chr13 115169878 3918851 0.03402670097471146 0.21422199650309195 chr14 107349540 3542922 0.03300360672248805 0.22831531109470848 chr15 102531392 3095358 0.030189368734991912 0.19930423197747982 chr16 90354753 2985235 0.03303904776320953 0.22100627913271198 chr17 81195210 2674476 0.032938839618741056 0.2407292099694501 chr18 78077248 3358963 0.043021021949953976 0.6055106244254628 chr19 59128983 1957058 0.033098117043548675 0.5412828169222516 chr20 63025520 2178665 0.03456798135104637 0.22021848344610162 chr21 48129895 1536914 0.03193262732029646 0.21592248802302674 chr22 51304566 1049692 0.02046001129801975 0.16194161569629784 chrMT 16571 8420 0.5081165892221351 0.9117627024394506 chrX 155270560 6524044 0.042017263285454756 0.2605848353253128 chrY 59373566 263340 0.004435307119670056 0.08338662176881996