BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524677.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 = 2,198,336 number of mapped reads = 2,036,864 (92.65%) number of supplementary alignments = 8,674 (0.39%) number of secondary alignments = 0 number of mapped bases = 120,052,683 bp number of sequenced bases = 120,016,043 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 97,582 duplication rate = 3.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6695 >>>>>>> ACTG content number of A's = 30,055,242 bp (25.04%) number of C's = 22,467,945 bp (18.72%) number of T's = 38,382,069 bp (31.98%) number of G's = 29,093,881 bp (24.24%) number of N's = 16,906 bp (0.01%) GC percentage = 42.96% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 600,268 number of insertions = 7,990 mapped reads with insertion percentage = 0.39% number of deletions = 22,952 mapped reads with deletion percentage = 1.12% homopolymer indels = 43.08% >>>>>>> Coverage mean coverageData = 0.0388X std coverageData = 0.3479X There is a 3.4% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 9645377 0.03869750438856479 0.6110379273680665 chr2 243199373 10125595 0.041634955201960984 0.503924445214426 chr3 198022430 7900040 0.039894672537853414 0.22306280858026525 chr4 191154276 7727964 0.040427889774226136 0.265733150636803 chr5 180915260 7224899 0.03993526582555833 0.22495276763304745 chr6 171115067 6892477 0.040279778518860644 0.2549308788004206 chr7 159138663 6609449 0.04153264125387304 0.4117995566857359 chr8 146364022 6080692 0.04154499115909783 0.36350666422621386 chr9 141213431 5049992 0.035761414224118666 0.286728759184535 chr10 135534747 5825957 0.04298496975096726 0.3623987144554769 chr11 135006516 5415120 0.04011006402090993 0.3070885065574884 chr12 133851895 5513813 0.04119338766178843 0.2298944864020582 chr13 115169878 3766985 0.03270807493605229 0.2072983346100744 chr14 107349540 3604942 0.03358134557446636 0.21673950516037305 chr15 102531392 3459293 0.03373886701938076 0.2090047614115421 chr16 90354753 3497940 0.03871340337790531 0.24349432692955741 chr17 81195210 3281384 0.04041351700426663 0.24560025666901378 chr18 78077248 3207925 0.04108655315310294 0.5318519309224435 chr19 59128983 2536065 0.042890387612450565 0.45940094842727036 chr20 63025520 2576511 0.04088044017724884 0.2316767168349842 chr21 48129895 1580707 0.03284251918687959 0.2391769629069383 chr22 51304566 1459674 0.028451151891626957 0.1885101528144531 chrMT 16571 8165 0.4927282602136262 0.730792664008979 chrX 155270560 6665643 0.04292921336794303 0.25645554058331554 chrY 59373566 396074 0.006670881112311833 0.2267504609827004