BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717013.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 40,342,045 number of mapped reads = 39,329,554 (97.49%) number of supplementary alignments = 33,571 (0.08%) number of secondary alignments = 0 number of mapped bases = 2,663,099,631 bp number of sequenced bases = 2,662,639,659 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,556,495 duplication rate = 1.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.8344 >>>>>>> ACTG content number of A's = 746,921,001 bp (28.05%) number of C's = 562,742,646 bp (21.13%) number of T's = 788,147,465 bp (29.6%) number of G's = 564,385,589 bp (21.2%) number of N's = 442,958 bp (0.02%) GC percentage = 42.33% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 9,772,996 number of insertions = 229,833 mapped reads with insertion percentage = 0.58% number of deletions = 242,234 mapped reads with deletion percentage = 0.61% homopolymer indels = 37.47% >>>>>>> Coverage mean coverageData = 0.8603X std coverageData = 12.7626X There is a 52.51% of reference with a coverageData >= 1X There is a 20.45% of reference with a coverageData >= 2X There is a 6.2% of reference with a coverageData >= 3X There is a 1.64% of reference with a coverageData >= 4X There is a 0.45% of reference with a coverageData >= 5X There is a 0.16% of reference with a coverageData >= 6X There is a 0.09% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% 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 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% 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 249235103 0.9999377413787868 25.61919651539619 chr2 243199373 227208323 0.9342471577835852 6.15176969305346 chr3 198022430 184899993 0.9337325726181624 7.209018586474846 chr4 191154276 151506760 0.7925889138885912 4.620473217451679 chr5 180915260 138832315 0.7673886381944784 1.5416841692005954 chr6 171115067 167065570 0.9763346555566612 5.868358235538078 chr7 159138663 151107669 0.9495346143507565 8.127949395805572 chr8 146364022 147141793 1.005313949352936 4.018724127069776 chr9 141213431 108023336 0.764965026591557 4.54257408148712 chr10 135534747 163325326 1.2050439434545888 43.10347448426798 chr11 135006516 107334313 0.7950306117076601 4.01143275164813 chr12 133851895 113049427 0.8445859283501366 1.6438458316955082 chr13 115169878 72050280 0.625600037537593 0.9219635592792482 chr14 107349540 69477545 0.6472085953978005 2.2316065019124363 chr15 102531392 74576839 0.7273561544936403 1.0093145349187498 chr16 90354753 76224353 0.8436119901738871 8.150877568120821 chr17 81195210 69687313 0.8582687697956567 2.942461593839302 chr18 78077248 67848654 0.8689939225316958 10.523407668722136 chr19 59128983 57393130 0.970642941719461 17.178296187123326 chr20 63025520 50303457 0.7981442596586271 1.9129266499504503 chr21 48129895 33354602 0.6930121497252384 4.482535399221527 chr22 51304566 36642318 0.714211635666112 1.8878917927922545 chrMT 16571 5216683 314.80797779252913 82.49042424302532 chrX 155270560 131385521 0.8461714893022863 2.8786337474690153 chrY 59373566 10209008 0.17194534011987758 6.595457738539286