Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.

ALE, Flask, Isolate	Predicted Mutations	Mean Coverage	Total Reads	Percent Mapped	Mapped Reads	Average Read Length
A11 F1 I1 R1	757	76.1	3598070	93.4%	3360597	108.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,765,829	(C)_5→4	intergenic (‑53/‑89)	yfjM ← / → rnlA	CP4‑57 prophage, uncharacterized protein/CP4‑57 prophage, RNase LS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,765,825	0	C	.	98.8%	326.9 / ‑2.7	81	intergenic (‑49/‑93)	yfjM/rnlA	CP4‑57 prophage, uncharacterized protein/CP4‑57 prophage, RNase LS
Reads supporting (aligned to +/- strand): ref base C (1/0); new base . (36/44); total (37/44)
Fisher's exact test for biased strand distribution p-value = 4.57e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.70e-01

TCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCA‑GGAAATGACAATCAGGAGTTACAAAAACTTAAATCTGGTC  >  NC_000913/2765686‑2765953

tCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCA‑TTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGc                                                                                                                                   >  2:1588655/1‑139 (MQ=255)

   tGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACTGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGccc                                                                                                                                 >  1:350605/1‑139 (MQ=255)

   tGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGccc                                                                                                                                 >  2:105449/1‑139 (MQ=255)

   tGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGccc                                                                                                                                 >  2:1624539/1‑139 (MQ=255)

    gTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGc                                                                                                                                   <  2:1639458/136‑1 (MQ=255)

    gTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGc                                                                                                                                   >  1:1639458/1‑136 (MQ=255)

               aataatTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTgg                                                                                                                    <  1:1624539/139‑1 (MQ=255)

                        tAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCA‑TTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAg                                                                                                          <  1:1588655/139‑1 (MQ=255)

                          aGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGc                                                                                                         >  2:89612/1‑139 (MQ=255)

                           gTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCa                                                                                                        <  2:665062/139‑1 (MQ=255)

                           gTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCa                                                                                                        <  1:155814/139‑1 (MQ=255)

                            tATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAg                                                                                                          <  1:1689931/136‑1 (MQ=255)

                            tATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAg                                                                                                          >  2:1689931/1‑136 (MQ=255)

                             aTCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCaaa                                                                                                      >  2:828640/1‑139 (MQ=255)

                              tCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGccactattc                                                                                                                           >  1:457626/1‑111 (MQ=255)

                              tCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTc                                                                                                                          <  2:457626/118‑1 (MQ=255)

                               cGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATc                                                                                                    >  1:533644/1‑139 (MQ=255)

                               cGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATc                                                                                                    >  1:1214609/1‑139 (MQ=255)

                                 aGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCaa                                                                                                  <  2:530306/139‑1 (MQ=255)

                                   ttGGTGCTTGGCGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATa                                                                                                <  2:1163543/139‑1 (MQ=255)

                                   ttGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATa                                                                                                <  1:105449/139‑1 (MQ=255)

                                   ttGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATa                                                                                                <  2:350605/139‑1 (MQ=255)

                                     gctgctTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCAGTAGACGATCCTGCCCTATAGTTGGATTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATaca                                                                                              >  2:1092460/1‑139 (MQ=255)

                                      ctgctTGGTGAGATCCGGAAGAGGTTACCGAAACGATGGACATCAACTCCCATTTTGTGGACTGCCCCCCCCGTAGACGATCCTGCCCCATAGTTGGAGTGCCCCGT‑TTCAGGTGGCTATATTTAGCAAATCAATacac                                                                                             >  1:1171259/1‑139 (MQ=255)

                                      ctgctTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATacac                                                                                             >  2:55358/1‑139 (MQ=255)

                                      ctgctTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATacac                                                                                             >  1:179150/1‑139 (MQ=255)

                                      ctgctTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATacac                                                                                             >  1:1720372/1‑139 (MQ=255)

                                      ctgctTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATa                                                                                                <  2:958786/136‑1 (MQ=255)

                                      ctgctTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATa                                                                                                >  1:958786/1‑136 (MQ=255)

                                                agaTCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAgggggg                                                                                   <  2:818575/139‑1 (MQ=255)

                                                            ggTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTaga                                                                       <  1:828640/139‑1 (MQ=255)

                                                             gTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATACTTGGAGCG‑CCCCTATCCAAGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTagct                                                                      >  1:818575/1‑137 (MQ=255)

                                                               tACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAg                                                                                                          <  1:48527/101‑1 (MQ=255)

                                                               tACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAg                                                                                                          >  2:48527/1‑101 (MQ=255)

                                                               tACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGta                                                                                 <  2:1453845/126‑1 (MQ=255)

                                                               tACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGta                                                                                 >  1:1423047/1‑126 (MQ=255)

                                                               tACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGta                                                                                 >  1:1453845/1‑126 (MQ=255)

                                                               tACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGta                                                                                 <  2:1423047/126‑1 (MQ=255)

                                                               tACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGta                                                                                 >  2:174678/1‑126 (MQ=255)

                                                               tACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGta                                                                                 <  1:174678/126‑1 (MQ=255)

                                                                 ccGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTTGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATa                                                                                                >  2:1396377/1‑109 (MQ=255)

                                                                 ccGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATa                                                                                                <  1:1396377/109‑1 (MQ=255)

                                                                 ccGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTc                                                                  <  2:179150/139‑1 (MQ=255)

                                                                 ccGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTc                                                                  >  1:1088969/1‑139 (MQ=255)

                                                                      aCGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAg                                                                                                          <  1:967650/94‑1 (MQ=255)

                                                                      aCGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAg                                                                                                          >  2:967650/1‑94 (MQ=255)

                                                                          tGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGt                                                         <  1:239395/139‑1 (MQ=255)

                                                                           ggACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATa                                                                                                >  2:108958/1‑99 (MQ=255)

                                                                           ggACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATa                                                                                                <  1:108958/99‑1 (MQ=255)

                                                                               atcatcCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTa                                                    <  2:1720372/139‑1 (MQ=255)

                                                                                 catcCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGta                                                                                 >  1:1272132/1‑108 (MQ=255)

                                                                                 catcCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGta                                                                                 <  2:1272132/108‑1 (MQ=255)

                                                                                 catcCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATg                                                  <  1:89612/139‑1 (MQ=255)

                                                                                             tgtgGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCA‑GGaaa                                     <  2:1088969/139‑1 (MQ=255)

                                                                                             tgtgGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCA‑GGaaa                                     <  1:55358/139‑1 (MQ=255)

                                                                                               tgGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCA‑GGAAATg                                   <  2:1214609/139‑1 (MQ=255)

                                                                                                ggACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCat                                                             >  2:1420125/1‑113 (MQ=255)

                                                                                                ggACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCat                                                             <  1:1420125/113‑1 (MQ=255)

                                                                                                ggACTGCCCCCACGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCA‑GGAAATGa                                  <  2:1171259/139‑1 (MQ=255)

                                                                                                 gACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGttt                                                                   <  2:272538/106‑1 (MQ=255)

                                                                                                 gACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGttt                                                                   >  1:272538/1‑106 (MQ=255)

                                                                                                    tGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGGAAATGACaa                               >  2:1746843/1‑139 (MQ=255)

                                                                                                     gCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAg                                                                                        <  2:1222571/81‑1 (MQ=255)

                                                                                                     gCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAg                                                                                        >  1:1222571/1‑81 (MQ=255)

                                                                                                      cccccccGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCA‑‑GGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCA‑GGAAATGACAATCAgg                          >  2:1559380/1‑139 (MQ=255)

                                                                                                                aGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGta                                                                                 <  1:970397/77‑1 (MQ=255)

                                                                                                                aGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGta                                                                                 >  2:970397/1‑77 (MQ=255)

                                                                                                                  aCGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATa                                                                                                >  2:113335/1‑60 (MQ=255)

                                                                                                                  aCGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATa                                                                                                <  1:113335/60‑1 (MQ=255)

                                                                                                                      tCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCA‑GGAAATGACAATCAGGAGTTACAAAAACtt            >  1:520497/1‑139 (MQ=255)

                                                                                                                       ccTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAggg                                                                                      >  2:1476876/1‑65 (MQ=255)

                                                                                                                       ccTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAggg                                                                                      <  1:1476876/65‑1 (MQ=255)

                                                                                                                         tGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATa                                                                                                >  2:1176185/1‑53 (MQ=255)

                                                                                                                         tGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATa                                                                                                <  1:1176185/53‑1 (MQ=255)

                                                                                                                           cccTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCTTATGTTTCTATGGGATCCA‑GGaaa                                     >  1:1182276/1‑109 (MQ=255)

                                                                                                                           cccTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTATCTATGGGATCCA‑GGaaa                                     <  2:1182276/109‑1 (MQ=255)

                                                                                                                                taGTTGGATTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCA‑GGAAATGACAATCAGGAGTTACAAAAACTTAAATCTGGTc  <  1:1092460/139‑1 (MQ=255)

                                                                                                                                taGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCa                                                                                         >  1:378320/1‑53 (MQ=255)

                                                                                                                                taGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCa                                                                                         <  2:378320/53‑1 (MQ=255)

                                                                                                                                taGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCA‑GGAAATg                                   <  1:932918/106‑1 (MQ=255)

                                                                                                                                taGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCA‑GGAAATg                                   >  2:932918/1‑106 (MQ=255)

                                                                                                                                 aGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGGAAATGACAATCAGGAGTTACAAAAACTTAAATCTGGTc  <  1:1746843/139‑1 (MQ=255)

                                                                                                                                   ttGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCA‑GGAAATGACAATCAGGAGTTACAAAAACTTAAAt        >  2:1656572/1‑130 (MQ=255)

                                                                                                                                   ttGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCA‑GGAAATGACAATCAGGAGTTACAAAAACTTAAAt        <  1:1656572/130‑1 (MQ=255)

                                                                                                                                     ggAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGta                                                                                 <  1:111026/56‑1 (MQ=255)

                                                                                                                                     ggAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGta                                                                                 >  2:111026/1‑56 (MQ=255)

                                                                                                                                     ggAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTa                                                                         >  1:1746660/1‑64 (MQ=255)

                                                                                                                                     ggAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTa                                                                         <  2:1746660/64‑1 (MQ=255)

TCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCA‑GGAAATGACAATCAGGAGTTACAAAAACTTAAATCTGGTC  >  NC_000913/2765686‑2765953

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A