BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173914.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 = 5,599,928 number of mapped reads = 5,452,480 (97.37%) number of supplementary alignments = 543,862 (9.71%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,728,490 number of mapped paired reads (second in pair) = 2,723,990 number of mapped paired reads (both in pair) = 5,355,288 number of mapped paired reads (singletons) = 97,192 number of mapped bases = 645,606,645 bp number of sequenced bases = 645,257,094 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,331,419 duplication rate = 65.76% >>>>>>> Insert size mean insert size = 846,146.0042 std insert size = 8,111,278.284 median insert size = 201 >>>>>>> Mapping quality mean mapping quality = 52.7445 >>>>>>> ACTG content number of A's = 195,247,445 bp (30.26%) number of C's = 125,552,723 bp (19.46%) number of T's = 194,689,100 bp (30.17%) number of G's = 129,760,677 bp (20.11%) number of N's = 7,149 bp (0%) GC percentage = 39.57% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 6,554,056 number of insertions = 66,196 mapped reads with insertion percentage = 1.17% number of deletions = 141,224 mapped reads with deletion percentage = 2.53% homopolymer indels = 42.81% >>>>>>> Coverage mean coverageData = 0.2085X std coverageData = 3.0692X There is a 4.06% of reference with a coverageData >= 1X There is a 3.24% of reference with a coverageData >= 2X There is a 2.55% of reference with a coverageData >= 3X There is a 2.13% of reference with a coverageData >= 4X There is a 1.67% of reference with a coverageData >= 5X There is a 1.38% of reference with a coverageData >= 6X There is a 1.05% of reference with a coverageData >= 7X There is a 0.86% of reference with a coverageData >= 8X There is a 0.65% of reference with a coverageData >= 9X There is a 0.54% of reference with a coverageData >= 10X There is a 0.41% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.23% of reference with a coverageData >= 14X There is a 0.18% of reference with a coverageData >= 15X There is a 0.16% 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 0.07% 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 0.02% 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% 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 58704885 0.2355255315492273 1.750816983123639 chr2 243199373 48408820 0.19904993751772543 8.864129253308839 chr3 198022430 39612887 0.2000424244869634 1.3461731012621743 chr4 191154276 40713357 0.21298690174213 1.6427938014311394 chr5 180915260 32245540 0.1782356004684182 1.2580714736290683 chr6 171115067 32172548 0.1880170376814334 1.354834988255483 chr7 159138663 56965691 0.3579626089984179 3.3676414092169233 chr8 146364022 64077502 0.4377954440197059 2.3506164704824437 chr9 141213431 22715757 0.16086116482786966 1.5944400370791805 chr10 135534747 29494647 0.21761686691310236 4.0114132031594645 chr11 135006516 26614594 0.19713562566120882 1.366012550371638 chr12 133851895 25146775 0.1878701455814279 1.2975879204736078 chr13 115169878 17044674 0.1479959369237154 1.1585118822490335 chr14 107349540 21449421 0.1998091561454292 1.3397828180069853 chr15 102531392 14900501 0.14532623335495143 1.120907099858742 chr16 90354753 14878852 0.16467149215714197 1.7300969080876252 chr17 81195210 15508327 0.19100051591713355 1.379178509007879 chr18 78077248 10591805 0.1356580216556813 2.0259978034936963 chr19 59128983 7812218 0.13212163652468029 1.3399362411273679 chr20 63025520 25068463 0.39775099039246326 1.9131479847871067 chr21 48129895 8028784 0.1668149078654753 1.3109021006448656 chr22 51304566 6400220 0.12474952034483637 1.0081197963201545 chrMT 16571 1443143 87.08846780520186 72.63301034627179 chrX 155270560 24491272 0.15773287608417205 1.1852821662623003 chrY 59373566 1115962 0.018795603417184004 0.8109073956572896