BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716755.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 = 504,028 number of mapped reads = 459,584 (91.18%) number of supplementary alignments = 1,954 (0.39%) number of secondary alignments = 0 number of mapped bases = 26,665,620 bp number of sequenced bases = 26,657,933 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,293 duplication rate = 1.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7468 >>>>>>> ACTG content number of A's = 6,643,636 bp (24.92%) number of C's = 5,001,761 bp (18.76%) number of T's = 8,542,075 bp (32.04%) number of G's = 6,469,734 bp (24.27%) number of N's = 727 bp (0%) GC percentage = 43.03% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 130,444 number of insertions = 1,811 mapped reads with insertion percentage = 0.39% number of deletions = 4,803 mapped reads with deletion percentage = 1.04% homopolymer indels = 42.92% >>>>>>> Coverage mean coverageData = 0.0086X std coverageData = 0.1137X There is a 0.82% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0% 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 2840243 0.011395129081744594 0.18028607394351073 chr2 243199373 2357171 0.00969233995516921 0.13651201923940665 chr3 198022430 2346575 0.011850046482108113 0.11256856315695186 chr4 191154276 1300172 0.006801689332861171 0.0875349510154197 chr5 180915260 1240764 0.0068582606022289105 0.08576033309329924 chr6 171115067 1905405 0.011135226332816151 0.12699608692284467 chr7 159138663 1490837 0.009368163411049896 0.1255316523671106 chr8 146364022 2000422 0.01366744349236317 0.12651532047772193 chr9 141213431 1016771 0.007200242872082047 0.09930897181326925 chr10 135534747 1352054 0.00997570017967422 0.11962169039648449 chr11 135006516 860532 0.006374003459210813 0.09079505489576992 chr12 133851895 1173065 0.008763902819605205 0.0973500646278184 chr13 115169878 587965 0.005105197732344563 0.07417707607824632 chr14 107349540 612597 0.0057065638101476725 0.07934961123718058 chr15 102531392 779572 0.007603251889918748 0.09064108542151696 chr16 90354753 563692 0.0062386535437709625 0.08564863765767487 chr17 81195210 600752 0.007398860105171229 0.08968084956387817 chr18 78077248 535370 0.006856927129398823 0.13545813084934194 chr19 59128983 511794 0.008655552218782454 0.12131451426732336 chr20 63025520 439139 0.006967637871135375 0.0863112360771184 chr21 48129895 248637 0.005165957665189172 0.07840053386046386 chr22 51304566 422352 0.008232249737771877 0.09354803598987718 chrMT 16571 3205 0.1934101744010621 0.4664289815966073 chrX 155270560 1397287 0.00899904656748839 0.10158491524752927 chrY 59373566 79247 0.0013347185513499392 0.04371450344036781