BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524403.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 = 1,058,464 number of mapped reads = 974,245 (92.04%) number of supplementary alignments = 3,655 (0.35%) number of secondary alignments = 0 number of mapped bases = 57,245,356 bp number of sequenced bases = 57,228,889 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 24,167 duplication rate = 1.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7074 >>>>>>> ACTG content number of A's = 15,374,612 bp (26.87%) number of C's = 10,753,013 bp (18.79%) number of T's = 17,245,605 bp (30.13%) number of G's = 13,848,123 bp (24.2%) number of N's = 7,536 bp (0.01%) GC percentage = 42.99% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 276,798 number of insertions = 4,888 mapped reads with insertion percentage = 0.5% number of deletions = 10,394 mapped reads with deletion percentage = 1.06% homopolymer indels = 41.81% >>>>>>> Coverage mean coverageData = 0.0185X std coverageData = 0.2033X There is a 1.72% of reference with a coverageData >= 1X There is a 0.09% 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 4690781 0.018819535859852483 0.386129334753098 chr2 243199373 4795302 0.019717575505426983 0.21890190778603383 chr3 198022430 3484636 0.017597178259048735 0.13902981480746684 chr4 191154276 3555428 0.018599782722098248 0.1541189335197101 chr5 180915260 3423937 0.018925639550804063 0.1443804005573038 chr6 171115067 3423329 0.02000600566635082 0.16277053303968078 chr7 159138663 3197125 0.020090183866883438 0.280111373354619 chr8 146364022 2947881 0.02014074879685938 0.19011357708720056 chr9 141213431 2455998 0.017392099197703084 0.17324627448824972 chr10 135534747 2735358 0.020181968539772315 0.1860883912801611 chr11 135006516 2617232 0.01938596800764787 0.1856702761188233 chr12 133851895 2558894 0.019117353549607946 0.14723111992513888 chr13 115169878 1801305 0.015640417714083192 0.1316385096815223 chr14 107349540 1787845 0.01665442627886435 0.14243648092740224 chr15 102531392 1654997 0.01614136868443179 0.13340903048782554 chr16 90354753 1729119 0.019137001016426885 0.15115857654391132 chr17 81195210 1550853 0.01910030160646176 0.15417609206577165 chr18 78077248 1577879 0.020209203582585288 0.27971347587560846 chr19 59128983 1186564 0.02006738387501101 0.26890715175502766 chr20 63025520 1217893 0.019323807245065175 0.14934989131311835 chr21 48129895 737081 0.015314411136778918 0.13893972725025341 chr22 51304566 680004 0.013254258889939738 0.12027747959649053 chrMT 16571 10047 0.6063001629352484 0.8278064680515848 chrX 155270560 3252291 0.020945960393264504 0.16536478014482603 chrY 59373566 173577 0.002923472711745156 0.09154321834456217