BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234092.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 = 5,339,925 number of mapped reads = 5,066,567 (94.88%) number of supplementary alignments = 33,215 (0.62%) number of secondary alignments = 0 number of mapped bases = 328,207,247 bp number of sequenced bases = 328,081,089 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 677,797 duplication rate = 11.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7344 >>>>>>> ACTG content number of A's = 84,575,589 bp (25.78%) number of C's = 59,245,650 bp (18.06%) number of T's = 106,746,878 bp (32.54%) number of G's = 77,481,540 bp (23.62%) number of N's = 31,432 bp (0.01%) GC percentage = 41.67% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 1,720,390 number of insertions = 20,831 mapped reads with insertion percentage = 0.41% number of deletions = 72,580 mapped reads with deletion percentage = 1.42% homopolymer indels = 44.42% >>>>>>> Coverage mean coverageData = 0.106X std coverageData = 1.0805X There is a 7.68% of reference with a coverageData >= 1X There is a 1.92% of reference with a coverageData >= 2X There is a 0.53% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 29049437 0.11654709979639329 1.9049385734214814 chr2 243199373 19324746 0.07946050913544091 2.0190453590572295 chr3 198022430 30460613 0.15382405417406503 0.5211237339301454 chr4 191154276 11470335 0.06000564172574408 0.38247450004001216 chr5 180915260 21180746 0.1170755081688521 0.4608451169699067 chr6 171115067 25100539 0.1466880704315769 0.8736965610012047 chr7 159138663 25789970 0.16205973780237176 1.815631558537466 chr8 146364022 19173239 0.13099693994470854 1.0419266492811539 chr9 141213431 12676170 0.08976603648982935 0.7158674265068228 chr10 135534747 16689485 0.12313805403716879 0.7378048334957635 chr11 135006516 14205456 0.1052205213561692 0.7775538472388317 chr12 133851895 8696264 0.06496930058405224 0.3809805045611108 chr13 115169878 16759240 0.1455175631947791 0.5604323985583733 chr14 107349540 14356558 0.13373655816317426 0.5568922086500218 chr15 102531392 6593763 0.06430969941381465 0.3797300185282804 chr16 90354753 10145555 0.11228579198263096 0.545489982733457 chr17 81195210 5430420 0.06688103891842881 0.4219944386542734 chr18 78077248 5394872 0.06909659520786389 1.7991415846279633 chr19 59128983 10373129 0.17543222415985069 1.1689508628837202 chr20 63025520 7838952 0.1243774267947333 0.5338090126879947 chr21 48129895 5582929 0.11599711572194371 0.4705555945228207 chr22 51304566 2034650 0.039658263554943625 0.24952453062726765 chrMT 16571 306414 18.490978214953834 10.946328678707918 chrX 155270560 8929396 0.05750862236859325 0.4409402030033433 chrY 59373566 644369 0.010852792638393996 0.24587229847963785