BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524311.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,526,533 number of mapped reads = 1,407,849 (92.23%) number of supplementary alignments = 5,464 (0.36%) number of secondary alignments = 0 number of mapped bases = 81,802,895 bp number of sequenced bases = 81,774,468 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 60,755 duplication rate = 3.27% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5957 >>>>>>> ACTG content number of A's = 19,680,786 bp (24.07%) number of C's = 16,349,886 bp (19.99%) number of T's = 26,655,745 bp (32.6%) number of G's = 19,086,254 bp (23.34%) number of N's = 1,797 bp (0%) GC percentage = 43.33% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 415,442 number of insertions = 6,060 mapped reads with insertion percentage = 0.43% number of deletions = 17,674 mapped reads with deletion percentage = 1.25% homopolymer indels = 43.06% >>>>>>> Coverage mean coverageData = 0.0264X std coverageData = 0.2636X There is a 2.38% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 6540675 0.02624135889314394 0.45026530545205545 chr2 243199373 6896063 0.028355595308216523 0.36155907515392616 chr3 198022430 5456030 0.02755258583585708 0.1811421074385968 chr4 191154276 5313814 0.027798562036875387 0.19807455751871583 chr5 180915260 4888780 0.02702248555483932 0.17872764859716175 chr6 171115067 4717323 0.02756813343619823 0.19988426931161576 chr7 159138663 4570302 0.02871899206542913 0.36449293080827455 chr8 146364022 4201468 0.028705606354545245 0.29750938813209726 chr9 141213431 3478324 0.02463167968774868 0.21984576216964943 chr10 135534747 3925187 0.028960743181230125 0.2543523477821719 chr11 135006516 3728061 0.027613933834126938 0.2183981970777763 chr12 133851895 3708782 0.027708102302175103 0.18391102493911735 chr13 115169878 2590441 0.02249234821625842 0.16473658110559555 chr14 107349540 2475777 0.023062763007647726 0.16931451102789305 chr15 102531392 2308795 0.02251793284928776 0.16376174300381163 chr16 90354753 2387805 0.02642699936327644 0.1900603187870348 chr17 81195210 2146429 0.026435414108787945 0.18351986314204086 chr18 78077248 2154757 0.027597758056226572 0.3840528778141728 chr19 59128983 1645157 0.02782319120895416 0.3310352737793514 chr20 63025520 1691219 0.02683387618221952 0.1806560171887098 chr21 48129895 1091455 0.022677277812469775 0.18083908421964354 chr22 51304566 937678 0.01827669685384338 0.1458902701943006 chrMT 16571 10389 0.6269386277231308 0.9610101094689217 chrX 155270560 4670927 0.030082502439612507 0.20511783919850304 chrY 59373566 267257 0.004501279239316702 0.13978589839109362