BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716573.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 = 1,874,446 number of mapped reads = 1,736,170 (92.62%) number of supplementary alignments = 42,812 (2.28%) number of secondary alignments = 0 number of mapped bases = 133,375,314 bp number of sequenced bases = 133,322,073 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 77,773 duplication rate = 3.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8649 >>>>>>> ACTG content number of A's = 33,943,494 bp (25.46%) number of C's = 27,216,783 bp (20.41%) number of T's = 40,024,059 bp (30.02%) number of G's = 32,132,575 bp (24.1%) number of N's = 5,162 bp (0%) GC percentage = 44.52% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 895,833 number of insertions = 11,578 mapped reads with insertion percentage = 0.66% number of deletions = 25,717 mapped reads with deletion percentage = 1.45% homopolymer indels = 37.77% >>>>>>> Coverage mean coverageData = 0.0431X std coverageData = 0.3616X There is a 3.6% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% 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 0.01% 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 14489815 0.05813351614478024 0.673120680511255 chr2 243199373 12150481 0.049960988180672655 0.36028758928525373 chr3 198022430 8456266 0.04270357655948369 0.23950905827218436 chr4 191154276 6731489 0.03521495381039763 0.32037801223543727 chr5 180915260 7904444 0.043691416633400634 0.2464918106393631 chr6 171115067 8460946 0.04944594388055845 0.2726970346971033 chr7 159138663 8508684 0.05346710748726097 0.5139999936232609 chr8 146364022 6863834 0.04689563668863923 0.37041845226163933 chr9 141213431 4035600 0.028578018191484915 0.25287479168832605 chr10 135534747 7214670 0.053231146696278556 0.4935637073009719 chr11 135006516 5638835 0.041767132187901214 0.3235962989145484 chr12 133851895 4681743 0.03497703936130303 0.2159777373910793 chr13 115169878 2543769 0.02208710336569081 0.16878416430527776 chr14 107349540 2605658 0.02427265175053382 0.1967631056236408 chr15 102531392 2624685 0.02559884293778046 0.18425680778427142 chr16 90354753 4826202 0.053413924998500076 0.28922941597837043 chr17 81195210 2604632 0.03207864109225162 0.24301081899380864 chr18 78077248 3873542 0.04961166151757808 0.40101803429794425 chr19 59128983 3284801 0.0555531455699145 0.5085985110929141 chr20 63025520 3086300 0.048969052536178996 0.2761217323476428 chr21 48129895 2065764 0.04292060059553423 0.29746825140478433 chr22 51304566 1903582 0.03710355916469501 0.23028086977464143 chrMT 16571 54525 3.290386820348802 2.8710473014111533 chrX 155270560 8302893 0.05347371066350247 0.28227369342183356 chrY 59373566 462154 0.007783834307678269 0.2941025671273748