BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716540.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 = 597,697 number of mapped reads = 547,543 (91.61%) number of supplementary alignments = 2,278 (0.38%) number of secondary alignments = 0 number of mapped bases = 31,776,112 bp number of sequenced bases = 31,766,604 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,961 duplication rate = 1.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3378 >>>>>>> ACTG content number of A's = 8,199,757 bp (25.81%) number of C's = 6,206,294 bp (19.54%) number of T's = 9,975,694 bp (31.4%) number of G's = 7,383,887 bp (23.24%) number of N's = 972 bp (0%) GC percentage = 42.78% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 158,856 number of insertions = 2,180 mapped reads with insertion percentage = 0.4% number of deletions = 5,948 mapped reads with deletion percentage = 1.08% homopolymer indels = 43.26% >>>>>>> Coverage mean coverageData = 0.0103X std coverageData = 0.1256X There is a 0.97% 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 2510457 0.010072019038219367 0.1953844552405565 chr2 243199373 2706854 0.011130184945008061 0.14309553308606188 chr3 198022430 2091510 0.010561985326611737 0.10723654866361233 chr4 191154276 2067124 0.010813904053080142 0.11162295956630075 chr5 180915260 1947375 0.010764017363709397 0.10789214139564973 chr6 171115067 1888931 0.011038951935191072 0.11682949594757652 chr7 159138663 1867920 0.011737688156899998 0.1432982426344342 chr8 146364022 1562443 0.010675048271083997 0.12348767165117241 chr9 141213431 1315826 0.009317994688479738 0.11235351094781203 chr10 135534747 1516561 0.011189462728697903 0.1273420907614282 chr11 135006516 1414102 0.010474324068921237 0.11611645383694644 chr12 133851895 1404441 0.010492499938084552 0.10742441275718863 chr13 115169878 1002771 0.008706886014066977 0.09737011765579144 chr14 107349540 948049 0.008831421168642176 0.0995155962151088 chr15 102531392 905782 0.008834191971176984 0.09790841472718782 chr16 90354753 918427 0.010164678331863738 0.10786950958240762 chr17 81195210 875381 0.010781190171193597 0.11162299249544053 chr18 78077248 831338 0.010647634506789993 0.1537845738939473 chr19 59128983 637070 0.010774242472595884 0.15388295799187282 chr20 63025520 659463 0.010463428147835989 0.1075232040425683 chr21 48129895 402553 0.008363886935552218 0.10005135134938409 chr22 51304566 361723 0.00705050306828441 0.08694800617855256 chrMT 16571 7933 0.4787278981352966 0.773140451659618 chrX 155270560 1833248 0.011806797115950377 0.11681114743302318 chrY 59373566 98830 0.0016645454645590936 0.05834151365546878