BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717030.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 = 963,877 number of mapped reads = 876,938 (90.98%) number of supplementary alignments = 4,350 (0.45%) number of secondary alignments = 0 number of mapped bases = 51,174,286 bp number of sequenced bases = 51,159,657 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 18,891 duplication rate = 1.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3113 >>>>>>> ACTG content number of A's = 12,780,708 bp (24.98%) number of C's = 9,886,724 bp (19.33%) number of T's = 16,099,093 bp (31.47%) number of G's = 12,392,564 bp (24.22%) number of N's = 568 bp (0%) GC percentage = 43.55% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 254,934 number of insertions = 2,983 mapped reads with insertion percentage = 0.34% number of deletions = 9,259 mapped reads with deletion percentage = 1.05% homopolymer indels = 41.24% >>>>>>> Coverage mean coverageData = 0.0165X std coverageData = 0.1729X There is a 1.54% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% 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 4203017 0.016862613955132333 0.24806727489125086 chr2 243199373 5043937 0.020739926003016464 0.21587440737713148 chr3 198022430 3455367 0.017449371770662546 0.1413547692608623 chr4 191154276 2847978 0.014898845370322765 0.13407539231588403 chr5 180915260 2706592 0.01496055114422078 0.12833486106599126 chr6 171115067 2782128 0.016258813725620082 0.14009389431811406 chr7 159138663 2412810 0.015161683242242647 0.23129305421835997 chr8 146364022 4931900 0.033696122398166946 0.2367571600268424 chr9 141213431 2106257 0.01491541551738092 0.1399262149296379 chr10 135534747 2443008 0.018024957098270896 0.22231798191743304 chr11 135006516 1535098 0.011370547477871364 0.12894859091588337 chr12 133851895 2332832 0.017428457027074587 0.14608920074258194 chr13 115169878 1313930 0.011408625439370526 0.11154753045487434 chr14 107349540 1615925 0.015052928964576839 0.13080054323531004 chr15 102531392 1191802 0.011623776647838742 0.11373739799011291 chr16 90354753 1559964 0.017264880354440237 0.1420238873634072 chr17 81195210 2153274 0.026519717111391176 0.17524844327669434 chr18 78077248 1081999 0.013858057599571132 0.19629605794646612 chr19 59128983 1033288 0.017475152582955806 0.22503904629922308 chr20 63025520 1151893 0.018276612394471318 0.14656472024157338 chr21 48129895 537647 0.011170749489480498 0.11728390865538747 chr22 51304566 768357 0.014976386312282614 0.12795713900988875 chrMT 16571 74558 4.49930601653491 3.2449784507497585 chrX 155270560 1774522 0.011428579893058928 0.12123447017719644 chrY 59373566 116203 0.0019571504261677664 0.061732358363015986