BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1264622.sorted.bam outfile = /home/yangyx/scDNA/SRP041470/SRP041470.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 = 1,409,616,214 number of mapped reads = 1,400,307,768 (99.34%) number of supplementary alignments = 7,962,194 (0.56%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 702,244,418 number of mapped paired reads (second in pair) = 698,063,350 number of mapped paired reads (both in pair) = 1,394,880,870 number of mapped paired reads (singletons) = 5,426,898 number of mapped bases = 140,576,366,817 bp number of sequenced bases = 140,544,085,153 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 528,815,486 duplication rate = 37.06% >>>>>>> Insert size mean insert size = 66,590.7706 std insert size = 2,485,015.6929 median insert size = 312 >>>>>>> Mapping quality mean mapping quality = 54.5898 >>>>>>> ACTG content number of A's = 43,477,331,131 bp (30.94%) number of C's = 26,692,747,269 bp (18.99%) number of T's = 43,401,604,386 bp (30.88%) number of G's = 26,964,825,039 bp (19.19%) number of N's = 7,577,328 bp (0.01%) GC percentage = 38.18% >>>>>>> Mismatches and indels general error rate = 0.0044 number of mismatches = 593,087,098 number of insertions = 15,371,881 mapped reads with insertion percentage = 1.08% number of deletions = 14,471,366 mapped reads with deletion percentage = 1.01% homopolymer indels = 48.47% >>>>>>> Coverage mean coverageData = 45.4103X std coverageData = 50.0571X There is a 89.31% of reference with a coverageData >= 1X There is a 87.34% of reference with a coverageData >= 2X There is a 85.59% of reference with a coverageData >= 3X There is a 83.96% of reference with a coverageData >= 4X There is a 82.4% of reference with a coverageData >= 5X There is a 80.9% of reference with a coverageData >= 6X There is a 79.44% of reference with a coverageData >= 7X There is a 78.01% of reference with a coverageData >= 8X There is a 76.62% of reference with a coverageData >= 9X There is a 75.26% of reference with a coverageData >= 10X There is a 73.91% of reference with a coverageData >= 11X There is a 72.6% of reference with a coverageData >= 12X There is a 71.3% of reference with a coverageData >= 13X There is a 70.02% of reference with a coverageData >= 14X There is a 68.76% of reference with a coverageData >= 15X There is a 67.52% of reference with a coverageData >= 16X There is a 66.3% of reference with a coverageData >= 17X There is a 65.09% of reference with a coverageData >= 18X There is a 63.9% of reference with a coverageData >= 19X There is a 62.73% of reference with a coverageData >= 20X There is a 61.57% of reference with a coverageData >= 21X There is a 60.42% of reference with a coverageData >= 22X There is a 59.29% of reference with a coverageData >= 23X There is a 58.18% of reference with a coverageData >= 24X There is a 57.08% of reference with a coverageData >= 25X There is a 55.99% of reference with a coverageData >= 26X There is a 54.92% of reference with a coverageData >= 27X There is a 53.87% of reference with a coverageData >= 28X There is a 52.83% of reference with a coverageData >= 29X There is a 51.81% of reference with a coverageData >= 30X There is a 50.8% of reference with a coverageData >= 31X There is a 49.8% of reference with a coverageData >= 32X There is a 48.82% of reference with a coverageData >= 33X There is a 47.86% of reference with a coverageData >= 34X There is a 46.91% of reference with a coverageData >= 35X There is a 45.98% of reference with a coverageData >= 36X There is a 45.06% of reference with a coverageData >= 37X There is a 44.15% of reference with a coverageData >= 38X There is a 43.26% of reference with a coverageData >= 39X There is a 42.39% of reference with a coverageData >= 40X There is a 41.53% of reference with a coverageData >= 41X There is a 40.69% of reference with a coverageData >= 42X There is a 39.86% of reference with a coverageData >= 43X There is a 39.04% of reference with a coverageData >= 44X There is a 38.24% of reference with a coverageData >= 45X There is a 37.46% of reference with a coverageData >= 46X There is a 36.69% of reference with a coverageData >= 47X There is a 35.93% of reference with a coverageData >= 48X There is a 35.19% of reference with a coverageData >= 49X There is a 34.46% of reference with a coverageData >= 50X There is a 33.74% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 10561000074 42.37100807062784 49.25839410509527 chr2 243199373 13358663358 54.928856078917605 53.97774673559997 chr3 198022430 10987333761 55.48529911990273 52.85160877189969 chr4 191154276 11542694730 60.384182721604404 53.020551655360144 chr5 180915260 10155104924 56.13183168738779 50.56342677457639 chr6 171115067 10026412579 58.594563031670376 55.09009501847142 chr7 159138663 7500327045 47.130765733528875 50.01863148128898 chr8 146364022 8368005504 57.17255777516144 52.48679238977685 chr9 141213431 5817504306 41.19653679401076 48.67719755501874 chr10 135534747 6042400085 44.581926175728206 46.51044223566408 chr11 135006516 6802066511 50.38324602791764 52.19671384375707 chr12 133851895 6712403166 50.1479875649127 52.69146831958252 chr13 115169878 5506174326 47.80915306691564 50.09623719981816 chr14 107349540 4713681230 43.90965466642894 51.79306592039768 chr15 102531392 3382744739 32.992283368200056 41.885021156404555 chr16 90354753 2539606547 28.107060920193096 36.54103669747965 chr17 81195210 2470427816 30.42578270319148 39.16918719168974 chr18 78077248 4152448805 53.183852035870935 49.32982965736168 chr19 59128983 986872116 16.69015880080332 25.675174112612726 chr20 63025520 2176791007 34.53824747499108 47.21919461047078 chr21 48129895 1613138714 33.51635639346398 48.38111882128121 chr22 51304566 778373212 15.171616732904436 27.468218285306403 chrMT 16571 47423 2.8618067708647636 7.7567004951170535 chrX 155270560 3813476142 24.56020086486453 31.954056620414626 chrY 59373566 568668697 9.57780937395608 23.70800747015221