BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173972.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 5,888,900 number of mapped reads = 5,758,572 (97.79%) number of supplementary alignments = 735,001 (12.48%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,882,559 number of mapped paired reads (second in pair) = 2,876,013 number of mapped paired reads (both in pair) = 5,681,448 number of mapped paired reads (singletons) = 77,124 number of mapped bases = 645,466,869 bp number of sequenced bases = 645,023,272 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,527,626 duplication rate = 63.65% >>>>>>> Insert size mean insert size = 1,049,005.9147 std insert size = 9,536,650.5706 median insert size = 149 >>>>>>> Mapping quality mean mapping quality = 52.5954 >>>>>>> ACTG content number of A's = 193,667,512 bp (30.02%) number of C's = 127,346,015 bp (19.74%) number of T's = 191,959,733 bp (29.76%) number of G's = 132,045,052 bp (20.47%) number of N's = 4,960 bp (0%) GC percentage = 40.21% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 5,495,812 number of insertions = 71,709 mapped reads with insertion percentage = 1.2% number of deletions = 187,469 mapped reads with deletion percentage = 3.18% homopolymer indels = 40.7% >>>>>>> Coverage mean coverageData = 0.2085X std coverageData = 3.6083X There is a 4.63% of reference with a coverageData >= 1X There is a 3.41% of reference with a coverageData >= 2X There is a 2.49% of reference with a coverageData >= 3X There is a 2% of reference with a coverageData >= 4X There is a 1.48% of reference with a coverageData >= 5X There is a 1.24% of reference with a coverageData >= 6X There is a 0.92% of reference with a coverageData >= 7X There is a 0.8% of reference with a coverageData >= 8X There is a 0.6% of reference with a coverageData >= 9X There is a 0.54% of reference with a coverageData >= 10X There is a 0.4% of reference with a coverageData >= 11X There is a 0.37% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.25% of reference with a coverageData >= 14X There is a 0.18% of reference with a coverageData >= 15X There is a 0.17% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.11% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% 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% 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 54299399 0.2178506066791304 1.95607742347248 chr2 243199373 55220359 0.22705798258780874 11.461100849315661 chr3 198022430 46639650 0.2355271067020034 1.448017231592271 chr4 191154276 45428086 0.23765142454882882 2.0617277785215227 chr5 180915260 38858142 0.21478642542370388 1.379469848807429 chr6 171115067 41603912 0.24313412447777027 1.6551151541895295 chr7 159138663 36729258 0.23080034296882335 2.0294332934118215 chr8 146364022 31997876 0.21861845255933182 2.2898250621974587 chr9 141213431 27175536 0.1924429978618677 1.7149692654880286 chr10 135534747 32101592 0.23685138099678602 2.464336025187999 chr11 135006516 30949370 0.22924352777165216 1.478187187333014 chr12 133851895 27411261 0.20478799347592352 1.3874863234504122 chr13 115169878 22849522 0.1983984215039283 1.3386928013773047 chr14 107349540 18617008 0.17342419911627008 1.2362133477771131 chr15 102531392 17830675 0.17390454427849766 1.2524056036226254 chr16 90354753 18993530 0.21021063496239095 1.6538664341508824 chr17 81195210 16790001 0.20678560964372159 1.4040897753861281 chr18 78077248 17280748 0.22132885626296664 2.249139517213448 chr19 59128983 11904353 0.20132855997201915 1.5653101620627807 chr20 63025520 14016536 0.2223946109448998 1.5034514393756795 chr21 48129895 9367866 0.19463715846460916 1.6529163904922164 chr22 51304566 7610867 0.14834677677616454 1.3794516393223404 chrMT 16571 508704 30.698449097821495 29.492748047960617 chrX 155270560 16311834 0.10505426141311013 0.9635838483789773 chrY 59373566 4970784 0.08372048935042911 1.443519300471521