BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506333.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 6,128,136 number of mapped reads = 4,641,328 (75.74%) number of supplementary alignments = 77,817 (1.27%) number of secondary alignments = 0 number of mapped bases = 365,339,362 bp number of sequenced bases = 365,186,032 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 537,505 duplication rate = 8.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.9871 >>>>>>> ACTG content number of A's = 102,957,576 bp (28.19%) number of C's = 68,041,265 bp (18.63%) number of T's = 106,582,273 bp (29.19%) number of G's = 87,510,278 bp (23.96%) number of N's = 94,640 bp (0.03%) GC percentage = 42.6% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 2,631,399 number of insertions = 29,903 mapped reads with insertion percentage = 0.63% number of deletions = 78,584 mapped reads with deletion percentage = 1.66% homopolymer indels = 44.85% >>>>>>> Coverage mean coverageData = 0.118X std coverageData = 0.8307X There is a 7.56% of reference with a coverageData >= 1X There is a 2.46% of reference with a coverageData >= 2X There is a 0.9% of reference with a coverageData >= 3X There is a 0.36% of reference with a coverageData >= 4X There is a 0.16% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% 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 26830006 0.10764268466958002 1.4401241768817632 chr2 243199373 29325028 0.1205801957392382 0.8781230299331799 chr3 198022430 23716398 0.11976622042260567 0.49335992588268257 chr4 191154276 24002157 0.12556432166864004 0.675616843924697 chr5 180915260 28373345 0.15683223736903124 0.5773432990563377 chr6 171115067 14373116 0.08399678796257024 0.46317832909879625 chr7 159138663 18560302 0.11662974697732631 1.0044620956577797 chr8 146364022 23488364 0.16047908276256578 1.2313379488991683 chr9 141213431 10468712 0.0741339681775737 0.8176731438383502 chr10 135534747 20898089 0.15418989936211708 0.9336677468055311 chr11 135006516 16180025 0.1198462524579184 0.795956249264335 chr12 133851895 15168109 0.11332009158331303 0.49729443506154636 chr13 115169878 7324526 0.06359758408357435 0.3548722430285031 chr14 107349540 10769001 0.10031716018531611 0.533792546202523 chr15 102531392 13662395 0.13325084867666676 0.5349188115417547 chr16 90354753 13054113 0.1444762180911501 0.6548175374999885 chr17 81195210 8190390 0.10087282242388436 0.536855584758657 chr18 78077248 6633908 0.08496595576729343 1.2872786441376525 chr19 59128983 8284155 0.14010311998770553 1.0770829113325957 chr20 63025520 9091440 0.14425013867398476 0.5870581691595667 chr21 48129895 6058010 0.1258679247066714 0.6429481683877352 chr22 51304566 4028117 0.07851381103194596 0.41812750059550985 chrMT 16571 36547 2.2054794520547945 2.2949125408120885 chrX 155270560 25620137 0.1650031854074591 0.6793249444628077 chrY 59373566 1202972 0.020261070389472648 0.66068665862304