BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063557.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,506,940 number of mapped reads = 2,259,471 (90.13%) number of supplementary alignments = 15,571 (0.62%) number of secondary alignments = 0 number of mapped bases = 148,141,046 bp number of sequenced bases = 148,073,182 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 99,901 duplication rate = 3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7475 >>>>>>> ACTG content number of A's = 40,248,650 bp (27.18%) number of C's = 27,355,891 bp (18.47%) number of T's = 46,425,273 bp (31.35%) number of G's = 34,040,416 bp (22.99%) number of N's = 2,952 bp (0%) GC percentage = 41.46% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,201,063 number of insertions = 11,150 mapped reads with insertion percentage = 0.49% number of deletions = 41,762 mapped reads with deletion percentage = 1.83% homopolymer indels = 45.28% >>>>>>> Coverage mean coverageData = 0.0479X std coverageData = 0.5705X There is a 4.08% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 15702612 0.06299928937789888 1.3723208192465497 chr2 243199373 17128136 0.07042837236262119 0.678506284249522 chr3 198022430 8380891 0.04232293786113018 0.2495527184442232 chr4 191154276 9028494 0.047231451939898014 0.24957240574306624 chr5 180915260 5224695 0.028879238821534457 0.19565860468110402 chr6 171115067 9961854 0.058217281357228465 0.35252970240892595 chr7 159138663 8787136 0.05521685198524007 0.6421403591439105 chr8 146364022 6247142 0.04268222418758074 0.5407679669124991 chr9 141213431 5254262 0.03720794801735254 0.4595678485130253 chr10 135534747 6199374 0.04574010825430618 0.5956367646663611 chr11 135006516 8607702 0.06375767818495516 0.4186045157578411 chr12 133851895 2702310 0.020188806441627145 0.1934679470338172 chr13 115169878 3764240 0.03268424057894721 0.20553197097442025 chr14 107349540 3911919 0.03644094795375928 0.2711781985565786 chr15 102531392 3291241 0.03209983728690624 0.21229592511316123 chr16 90354753 3113399 0.03445750109017508 0.2563728429903917 chr17 81195210 5400556 0.06651323397032904 0.3321918908299642 chr18 78077248 4460604 0.05713065091638476 0.7641898830915801 chr19 59128983 3952854 0.06685137811350485 0.9252809095983554 chr20 63025520 2797490 0.04438662306951216 0.2576908521421154 chr21 48129895 2410711 0.05008760147928849 0.26722976017972405 chr22 51304566 1552579 0.03026200436039163 0.1945449445184843 chrMT 16571 18204 1.0985456520427253 1.291053578264132 chrX 155270560 9880306 0.06363283548407374 0.34440329544497955 chrY 59373566 362335 0.006102631598715159 0.15540938664618437