BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975262.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 5,977,258 number of mapped reads = 5,782,989 (96.75%) number of supplementary alignments = 88,246 (1.48%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,911,288 number of mapped paired reads (second in pair) = 2,871,701 number of mapped paired reads (both in pair) = 5,720,486 number of mapped paired reads (singletons) = 62,503 number of mapped bases = 793,383,545 bp number of sequenced bases = 792,730,788 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 739,738 duplication rate = 9.65% >>>>>>> Insert size mean insert size = 70,717.3047 std insert size = 2,486,963.3526 median insert size = 200 >>>>>>> Mapping quality mean mapping quality = 53.5996 >>>>>>> ACTG content number of A's = 226,816,923 bp (28.61%) number of C's = 161,061,678 bp (20.32%) number of T's = 229,447,508 bp (28.94%) number of G's = 175,335,684 bp (22.12%) number of N's = 68,995 bp (0.01%) GC percentage = 42.44% >>>>>>> Mismatches and indels general error rate = 0.0124 number of mismatches = 9,385,467 number of insertions = 153,909 mapped reads with insertion percentage = 2.48% number of deletions = 329,580 mapped reads with deletion percentage = 5.44% homopolymer indels = 46.4% >>>>>>> Coverage mean coverageData = 0.2563X std coverageData = 2.3633X There is a 12.22% of reference with a coverageData >= 1X There is a 6.64% of reference with a coverageData >= 2X There is a 2.71% of reference with a coverageData >= 3X There is a 1.43% of reference with a coverageData >= 4X There is a 0.71% of reference with a coverageData >= 5X There is a 0.39% of reference with a coverageData >= 6X There is a 0.22% of reference with a coverageData >= 7X There is a 0.13% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% 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 54319402 0.21793085923745803 2.262325189189676 chr2 243199373 68193938 0.2804034285071944 3.199545122477221 chr3 198022430 60163730 0.3038228043156525 0.931012242291365 chr4 191154276 64850210 0.3392558689087342 2.6770663858821426 chr5 180915260 45790189 0.2531029665490904 0.8431985319109903 chr6 171115067 37571148 0.21956656803342747 1.6083278470552422 chr7 159138663 59259617 0.3723772456225801 3.1132337775024945 chr8 146364022 44835155 0.30632633885942273 1.2939675445124743 chr9 141213431 29009710 0.20543166322472542 3.4198395031491975 chr10 135534747 52848850 0.38992842182381465 5.520054324634435 chr11 135006516 33140135 0.24547063343224115 1.523979418658754 chr12 133851895 39248687 0.2932247391790755 0.9167185135211611 chr13 115169878 16309860 0.1416156748902695 0.612493847235346 chr14 107349540 20934118 0.19500892132374298 0.7894495508474635 chr15 102531392 16651576 0.16240466139384901 0.6593089551732856 chr16 90354753 23328714 0.2581902249237514 2.398754355217466 chr17 81195210 24544035 0.30228427268061747 2.2930983278757178 chr18 78077248 15892796 0.203552205118705 3.2151213240416356 chr19 59128983 8862161 0.14987846146449027 1.2211286752215778 chr20 63025520 17765233 0.2818736442000003 1.220495432501146 chr21 48129895 12804787 0.2660464353807545 1.7177628394736408 chr22 51304566 9045345 0.17630682228166591 0.7315770318616148 chrMT 16571 477508 28.81588316939231 16.144458739755702 chrX 155270560 33081368 0.21305628059820225 0.9074037524270192 chrY 59373566 4455273 0.07503798912802374 4.095962170815184