BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714132.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 649,660 number of mapped reads = 519,341 (79.94%) number of supplementary alignments = 17,571 (2.7%) number of secondary alignments = 0 number of mapped bases = 68,089,427 bp number of sequenced bases = 66,509,785 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 457,972 duplication rate = 43.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.645 >>>>>>> ACTG content number of A's = 18,565,904 bp (27.91%) number of C's = 13,625,571 bp (20.49%) number of T's = 17,650,943 bp (26.54%) number of G's = 16,666,837 bp (25.06%) number of N's = 530 bp (0%) GC percentage = 45.55% >>>>>>> Mismatches and indels general error rate = 0.0465 number of mismatches = 2,893,983 number of insertions = 74,151 mapped reads with insertion percentage = 13.68% number of deletions = 258,968 mapped reads with deletion percentage = 46.29% homopolymer indels = 30.04% >>>>>>> Coverage mean coverageData = 0.022X std coverageData = 5.231X There is a 0.06% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3994471 0.016025921957482304 3.1309666722964966 chr2 243199373 6541018 0.026895702564167383 12.063658438630469 chr3 198022430 2828911 0.0142858109558599 4.776598330544101 chr4 191154276 3121114 0.016327722640115044 2.4899556452749128 chr5 180915260 6397624 0.03536254487321854 6.24664952620163 chr6 171115067 4693361 0.027428099011292794 4.298599223232831 chr7 159138663 2853943 0.017933687176949577 3.3681952696621758 chr8 146364022 6724375 0.04594281373328208 9.280593969808681 chr9 141213431 1442318 0.010213745178388875 1.6115995518527575 chr10 135534747 3393248 0.025036000546782296 3.65628004714336 chr11 135006516 1624597 0.012033471036316499 1.8453681516324218 chr12 133851895 4690993 0.03504614559248489 4.652098953642397 chr13 115169878 2065412 0.017933612814975804 2.9542978510079454 chr14 107349540 1742963 0.01623633412867908 4.356025706997171 chr15 102531392 965643 0.009418022921214218 1.7838335447752751 chr16 90354753 1081042 0.01196441763279459 1.515705553372613 chr17 81195210 852268 0.010496530521935962 2.4819127960073106 chr18 78077248 1477784 0.0189272039916161 2.4307932232029157 chr19 59128983 1204088 0.020363752916230608 2.8107230245390773 chr20 63025520 1221523 0.019381402961847836 3.45210939904745 chr21 48129895 229894 0.004776532340243003 0.582786766325868 chr22 51304566 704972 0.013740921227167188 1.988583221997736 chrMT 16571 501675 30.27427433468107 243.5042877779285 chrX 155270560 7456960 0.048025588366526144 5.041112833232628 chrY 59373566 279230 0.004702934635928723 1.1677721651758501