BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548972.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 = 7,232,433 number of mapped reads = 3,248,879 (44.92%) number of secondary alignments = 0 number of mapped bases = 128,443,244 bp number of sequenced bases = 128,426,938 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 72,165 duplication rate = 1.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6414 >>>>>>> ACTG content number of A's = 39,484,220 bp (30.74%) number of C's = 24,496,581 bp (19.07%) number of T's = 39,501,665 bp (30.76%) number of G's = 24,938,489 bp (19.42%) number of N's = 5,983 bp (0%) GC percentage = 38.49% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 398,538 number of insertions = 4,977 mapped reads with insertion percentage = 0.15% number of deletions = 12,974 mapped reads with deletion percentage = 0.4% homopolymer indels = 45.55% >>>>>>> Coverage mean coverageData = 0.0415X std coverageData = 0.3167X There is a 3.65% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.05% 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 10221229 0.04100783764947972 0.5271300367402216 chr2 243199373 11154082 0.04586394225613402 0.2937396745850036 chr3 198022430 9150419 0.046209002687220835 0.23810180736849787 chr4 191154276 9039520 0.047289133097917206 0.244478127267046 chr5 180915260 8384283 0.0463437025710269 0.24002461783964457 chr6 171115067 7849819 0.04587450501947909 0.2650291228305342 chr7 159138663 7300242 0.0458734657083301 0.4288686639253497 chr8 146364022 6809850 0.04652680287782745 0.49092471303834856 chr9 141213431 5516588 0.03906560417755164 0.2726220668346964 chr10 135534747 6009141 0.044336534600975794 0.27824265599820586 chr11 135006516 5894530 0.0436610778104962 0.2831299691361287 chr12 133851895 5838118 0.04361625212702443 0.23760377955230255 chr13 115169878 4459306 0.03871937764838129 0.2169802182469625 chr14 107349540 4073783 0.037948769971440956 0.2487491817022039 chr15 102531392 3654149 0.035639319126770465 0.2082662927708607 chr16 90354753 3333945 0.0368983909457425 0.2228209711120346 chr17 81195210 3094475 0.038111546235301316 0.2248792785135304 chr18 78077248 3526541 0.04516733222974252 0.44399613885409783 chr19 59128983 2151337 0.03638379844956914 0.4810618404203545 chr20 63025520 2464172 0.03909800347541758 0.22281541718464162 chr21 48129895 1737461 0.036099413888187375 0.2277755212156613 chr22 51304566 1261542 0.024589273399174646 0.191026391592549 chrMT 16571 3913 0.23613541729527487 0.5375270112091299 chrX 155270560 4451657 0.028670322307074825 0.21611159336665778 chrY 59373566 1063142 0.017905981931420456 0.19481866864668224