BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716170.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 = 448,158 number of mapped reads = 418,574 (93.4%) number of supplementary alignments = 8,008 (1.79%) number of secondary alignments = 0 number of mapped bases = 33,432,806 bp number of sequenced bases = 33,417,250 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,866 duplication rate = 1.19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.9106 >>>>>>> ACTG content number of A's = 8,806,488 bp (26.35%) number of C's = 6,553,545 bp (19.61%) number of T's = 9,888,563 bp (29.59%) number of G's = 8,166,298 bp (24.44%) number of N's = 2,356 bp (0.01%) GC percentage = 44.05% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 212,480 number of insertions = 2,927 mapped reads with insertion percentage = 0.69% number of deletions = 8,126 mapped reads with deletion percentage = 1.91% homopolymer indels = 42.83% >>>>>>> Coverage mean coverageData = 0.0108X std coverageData = 0.1293X There is a 1.02% of reference with a coverageData >= 1X There is a 0.04% 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 2685106 0.010772715386735184 0.1996825354552029 chr2 243199373 2850108 0.011719224292572498 0.13871898610198408 chr3 198022430 2205343 0.011136834347502957 0.10868211690697613 chr4 191154276 2176517 0.011386180029789132 0.11984770929194127 chr5 180915260 2039029 0.011270630238709549 0.10986995426229472 chr6 171115067 1896068 0.011080660711192661 0.11218736735881406 chr7 159138663 1842106 0.01157547741870874 0.14953151195791625 chr8 146364022 1748490 0.011946173493373938 0.14267112600171902 chr9 141213431 1366463 0.009676579559914524 0.11969465640836302 chr10 135534747 1606678 0.011854362335586165 0.13512803870938297 chr11 135006516 1506786 0.011160839081278122 0.12179671034633495 chr12 133851895 1456085 0.010878329365452764 0.10776772451316638 chr13 115169878 1048662 0.009105349577603963 0.09834515387014707 chr14 107349540 1007879 0.009388759374283299 0.10158553039260333 chr15 102531392 968877 0.0094495644807007 0.10028457203706449 chr16 90354753 967605 0.010708955178041381 0.1100765690427895 chr17 81195210 900523 0.011090838979294469 0.11380110608516947 chr18 78077248 921847 0.011806858254020428 0.16422425196785342 chr19 59128983 653124 0.01104575060930779 0.15397697757210135 chr20 63025520 734942 0.011661022392199223 0.11256914819698667 chr21 48129895 460013 0.009557739529662386 0.10496263826226634 chr22 51304566 406515 0.007923563762336475 0.09278405871346837 chrMT 16571 2003 0.12087381570213022 0.3545347280623535 chrX 155270560 1881683 0.012118736481661431 0.11844432214166105 chrY 59373566 100354 0.0016902134529025931 0.06571058249912329