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
A9 F1 I2 R1	78	48.0	2243616	94.8%	2126947	114.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,648,024	T→C	intergenic (‑236/‑39)	dinQ ← / → agrA	UV‑inducible membrane toxin, DinQ‑AgrB type I toxin‑antitoxin system/inactive antisense sRNA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,648,024	0	T	C	98.6%	256.2 / ‑4.5	71	intergenic (‑236/‑39)	dinQ/agrA	UV‑inducible membrane toxin, DinQ‑AgrB type I toxin‑antitoxin system/inactive antisense sRNA
Reads supporting (aligned to +/- strand): ref base T (0/1); new base C (38/32); total (38/33)
Fisher's exact test for biased strand distribution p-value = 4.65e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.25e-01

GCCAGAGCATCAGTTAACGGCACCACCCGTACTTCTGACCAGGACTTTGAAAGCGTTTATGCGCATTGCCAGAGTGAAAATGCCTCAGAGCTAACTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGTCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAGATGATGGCTATCTCACTCCAGTCAGAGCCACCAACTCAGGGCTGGAAAGTAAAAAACCGACGCAAAGTCGGTTTTTTTACATCCGGATTCGGA  >  NC_000913/3647888‑3648159

gCCAGAGCATCAGTTAACGGCACCACCCGTACTTCTGACCAGGACTTTGAAAGCGTTTATGCGCATTGCCAGAGTGAAAATGCCTCAGAGCTAACTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGccc                                                                                                                                       >  1:89048/1‑139 (MQ=255)

            gTTAACGGCACCACCCGTACTTCTGACCAGGACTTTGAAAGCGTTTATGCGCATTGCCAGAGTGAAAATGCCTCAGAGCTAACTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGTCCTTGCAATAGttt                                                                                                                           <  2:229903/139‑1 (MQ=255)

            gTTAACGGCACCACCCGTACTTCTGACCAGGACTTTGAAAGCGTTTATGCGCATTGCCAGAGTGAAAATGCCTCAGAGCTAACTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGttt                                                                                                                           <  2:258645/139‑1 (MQ=255)

            gTTAACGGCACCACCCGTACTTCTGACCAGGACTTTGAAAGCGTTTATGCGCATTGCCAGAGTGAAAATGCCTCAGAGCTAACTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGttt                                                                                                                           <  1:293235/139‑1 (MQ=255)

            gTTAACGGCACCACCCGTACTTCTGACCAGGACTTTGAAAGCGTTTATGCGCATTGCCAGAGTGAAAATGCCTCAGAGCTAACTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGttt                                                                                                                           <  1:625646/139‑1 (MQ=255)

               aaCGGCACCACCCGTACTTCTGACCAGGACTTTGAAAGCGTTTATGCGCATTGCCAGAGTGAAAATGCCTCAGAGCTAACTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAg                                                                                                                        >  1:1029664/1‑139 (MQ=255)

                 cGGCACCACCCGTACTTCTGACCAGGACTTTGAAAGCGTTTATGCGCATTGCCAGAGTGAAAATGCCTCAGAGCTAACTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTa                                                                                                                      <  2:1004793/139‑1 (MQ=255)

                 cGGCACCACCCGTACTTCTGACCAGGACTTTGAAAGCGTTTATGCGCATTGCCAGAGTGAAAATGCCTCAGAGCTAACTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTa                                                                                                                      <  1:964432/139‑1 (MQ=255)

                 cGGCACCACCCGTACTTCTGACCAGGACTTTGAAAGCGTTTATGCGCATTGCCAGAGTGAAAATGCCTCAGAGCTAACTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTa                                                                                                                      <  1:688770/139‑1 (MQ=255)

                     accaccCGTACTTCTGACCAGGACTTTGAAAGCGTTTATGCGCATTGCCAGAGTGAAAATGCCTCAGAGCTAACTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGt                                                                                                                  >  1:662086/1‑139 (MQ=255)

                       caccCGTACTTCTGACCAGGACTTTGAAAGCGTTTATGCGCATTGCCAGAGTGAAAATGCCTCAGAGCTAACTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCa                                                                                                                                  >  2:904025/1‑121 (MQ=255)

                       caccCGTACTTCTGACCAGGACTTTGAAAGCGTTTATGCGCATTGCCAGAGTGAAAATGCCTCAGAGCTAACTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCa                                                                                                                                  <  1:904025/121‑1 (MQ=255)

                       caccCGTACTTCTGACCAGGACTTTGAAAGCGTTTATGCGCATTGCCAGAGTGAAAATGCCTCAGAGCTAACTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTAt                                                                                                                     >  2:822890/1‑134 (MQ=255)

                       caccCGTACTTCTGACCAGGACTTTGAAAGCGTTTATGCGCATTGCCAGAGTGAAAATGCCTCAGAGCTAACTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTAt                                                                                                                     <  1:822890/134‑1 (MQ=255)

                       caccCGTACTTCTGACCAGGACTTTGAAAGCGTTTATGCGCATTGCCAGAGTGAAAATGCCTCAGAGCTAACTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTAt                                                                                                                >  1:963962/1‑139 (MQ=255)

                               cTTCTGACCAGGACTTTGAAAGCGTTTATGCGCATTGCCAGAGTGAAAATGCCTCAGAGCTAACTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTg                                                                                                        <  1:488317/139‑1 (MQ=255)

                               cTTCTGACCAGGACTTTGAAAGCGTTTATGCGCATTGCCAGAGTGAAAATGCCTCAGAGCTAACTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTg                                                                                                        <  1:527072/139‑1 (MQ=255)

                                ttCTGACCAGGACTTTGAAAGCGTTTATGCGCATTGCCAGAGTGAAAATGCCTCAGAGCTAACTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGa                                                                                                       <  1:937446/139‑1 (MQ=255)

                                ttCTGACCAGGACTTTGAAAGCGTTTATGCGCATTGCCAGAGTGAAAATGCCTCAGAGCTAACTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGa                                                                                                       <  2:802105/139‑1 (MQ=255)

                                 tCTGACCAGGACTTTGAAAGCGTTTATGCGCATTGCCAGAGTGAAAATGCCTCAGAGCTAACTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGAt                                                                                                      <  2:431145/139‑1 (MQ=255)

                                    gACCGGGACTTTGAAAGCGTTTATGCGCATTGCCAGAGTGAAAATGCCTCAGAGCTAACTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGa                                                                                                       >  1:66542/1‑135 (MQ=255)

                                    gACCGGGACTTTGAAAGCGTTTATGCGCATTGCCAGAGTGAAAATGCCTCAGAGCTAACTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGa                                                                                                       <  2:66542/135‑1 (MQ=255)

                                        aGGACTTTGAAAGCGTTTATGCGCATTGCCAGAGTGAAAATGCCTCAGAGCTAACTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGt                                                                                                  <  1:655776/136‑1 (MQ=255)

                                        aGGACTTTGAAAGCGTTTATGCGCATTGCCAGAGTGAAAATGCCTCAGAGCTAACTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGt                                                                                                  >  2:655776/1‑136 (MQ=255)

                                          gACTTTGAAAGCGTTTATGCGCATTGCCAGAGTGAAAATGCCTCAGAGCTAACTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAgat                                                                                             <  2:571783/139‑1 (MQ=255)

                                             tttGAAAGCGTTTATGCGCATTGCCAGAGTGAAAATGCCTCAGAGCTAACTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAgatgat                                                                                          <  1:356201/139‑1 (MQ=255)

                                               agAAAACGTTTATGCGCATTGCCAGAGTGAAAATGCCTCAGCGCTAACTTGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAATTTCAGTATGGTATTAGCATTGATGCGTTAGATGATgg                                                                                        >  1:381945/2‑139 (MQ=255)

                                                gAAAGCGTTTATGCGCATTGCCAGAGTGAAAATGCCTCAGAGCTAACTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAGATGATGGc                                                                                       <  1:940519/139‑1 (MQ=255)

                                                                  tGCCAGAGTGAAAATGCCTCAGAGCTAACTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAGATGATGGCTATCTCACTCCAGTCaga                                                                     >  2:532970/1‑139 (MQ=255)

                                                                            aaaaTGCCTCAGAGCTAACTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTa                                                                                                                      >  2:476377/1‑80 (MQ=255)

                                                                            aaaaTGCCTCAGAGCTAACTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTa                                                                                                                      <  1:476377/80‑1 (MQ=255)

                                                                            aaaaTGCCTCAGAGCTAACTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAga                                                                                              >  2:238994/1‑104 (MQ=255)

                                                                            aaaaTGCCTCAGAGCTAACTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAga                                                                                              <  1:238994/104‑1 (MQ=255)

                                                                            aaaaTGCCTCAGAGCTAACTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAGATGATgg                                                                                        <  1:704563/110‑1 (MQ=255)

                                                                            aaaaTGCCTCAGAGCTAACTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAGATGATgg                                                                                        >  2:704563/1‑110 (MQ=255)

                                                                            aaaaTGCCTCAGAGCTAACTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAGATGATGGCTATCTCACTCCAGTCAGAGCCACCAACt                                                           >  1:1028760/1‑139 (MQ=255)

                                                                              aaTGCCTCAGAGCTAACTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAGATGATGGCTATCTCACTCCAGTCAGAGCCACCAACTCa                                                         >  2:478344/1‑139 (MQ=255)

                                                                                        agCTAACTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTa                                                                                                                      >  1:842174/1‑68 (MQ=255)

                                                                                        agCTAACTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTa                                                                                                                      <  2:842174/68‑1 (MQ=255)

                                                                                             aCTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAGATGATgg                                                                                        <  2:613059/93‑1 (MQ=255)

                                                                                             aCTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAGATGATgg                                                                                        >  1:613059/1‑93 (MQ=255)

                                                                                             aCTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAGATGATGGCTATCTCACTCCAGTCAGAGCCACCAACTCAGGGCTGGAAAGTaaa                                          >  2:1006024/1‑139 (MQ=255)

                                                                                                ggATAATCATACAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATg                                                                                                     >  1:769754/1‑77 (MQ=255)

                                                                                                ggATAATCATACAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATg                                                                                                     <  2:769754/77‑1 (MQ=255)

                                                                                                      tCATACAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAGATGATGGCTATCTCACTCCAGTCAGAGCCACCAACTCAGGGCTGGAAAGTAAAAAACCGACg                                 >  2:754137/1‑139 (MQ=255)

                                                                                                       cATACAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAgatg                                                                                            <  1:577894/79‑1 (MQ=255)

                                                                                                       cATACAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAgatg                                                                                            >  2:577894/1‑79 (MQ=255)

                                                                                                           cAGTACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAGATGATGGCTATCTCACTCCAGTCAGAGCCACCAACTCAGGGCTGGAAAGTAAAAAACCGACGCAAAg                            >  2:68300/1‑139 (MQ=255)

                                                                                                              tACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAGATGATGGCTATCTCACTCCAGTCAGAGCCACCAACTCAGGGCTGGAAAGTAAAAAACCGACGCAAAGTCg                         >  2:981152/1‑139 (MQ=255)

                                                                                                              tACATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAGATGATGGCTATCTCACTCCAGTCAGAGCCACCAACTCAGGGCTGGAAAGTAAAAAACCGACGCAAAGTCg                         >  1:613444/1‑139 (MQ=255)

                                                                                                                cATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAGATGATGGCTATCTCACTCCAGTCAGAGCCACCAACTCAGGGCTGGAAAGTAAAAAACCGACGCAAAGTCGGt                       >  1:1112159/1‑139 (MQ=255)

                                                                                                                cATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAGATGATGGCTATCTCACTCCAGTCAGAGCCACCAACTCAGGGCTGGAAAGTAAAAAACCGACGCAAAGTCGGt                       >  1:502643/1‑139 (MQ=255)

                                                                                                                cATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAGATGATGGCTATCTCACTCCAGTCAGAGCCACCAACTCAGGGCTGGAAAGTAAAAAACCGACGCAAAGTCGGt                       >  2:1026913/1‑139 (MQ=255)

                                                                                                                cATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAGATGATGGCTATCTCACTCCAGTCAGAGCCACCAACTCAGGGCTGGAAAGTAAAAAACCGACGCAAAGTCGGt                       >  1:837748/1‑139 (MQ=255)

                                                                                                                cATGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTGAGATGATGGCTATCTCACTCCAGTCAGAGCCACCAACTCAGGGCTGGAAAGTAAAAAACCGACGCAAAGTCGGt                       >  2:601681/1‑139 (MQ=255)

                                                                                                                 aTGCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAGATGATGGCTATCTCACTCCAGTCAGAGCCACCAACTCAGGGCTGGAAAGTAAAAAACCGACGCAAAGTCGGtt                      <  1:1006024/139‑1 (MQ=255)

                                                                                                                   gCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAGATGATGGCTATCTCACTCCAGTCAGAGccac                                                                <  1:768584/95‑1 (MQ=255)

                                                                                                                   gCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAGATGATGGCTATCTCACTCCAGTCAGAGccac                                                                >  2:768584/1‑95 (MQ=255)

                                                                                                                   gCAGGTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAGATGATGGCTATCTCACTCCAGTCAGAGCCACCAACTCAGGGCTGGAAAGTAAAAAACCGACGCAAAGTCGGtttt                    >  1:229478/1‑139 (MQ=255)

                                                                                                                      ggTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAGATGATGGCTATCTCACTCCAGTCAGAGCCACCAACTCAGGGCTGGAAAGTAAAAAACCGACGCAAAGTCGGttttttt                 >  2:537370/1‑139 (MQ=255)

                                                                                                                      ggTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAGATGATGGCTATCTCACTCCAGTCAGAGCCACCAACTCAGGGCTGGAAAGTAAAAAACCGACGCAAAGTCGGttttttt                 >  1:1018408/1‑139 (MQ=255)

                                                                                                                       gTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAGATGATGGCTATCTCACTCCAGTCAGAGCCACCAACTCAGGGCTGGAAAGTAAAAAACCGACGCAAAGTCGGTTTTTTTa                >  1:782641/1‑139 (MQ=255)

                                                                                                                       gTTATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAGATGATGGCTATCTCACTCCAGTCAGAGCCACCAACTCAGGGCTGGAAAGTAAAAAACCGACGCAAAGTCGGTTTTTTTa                >  1:1093042/1‑139 (MQ=255)

                                                                                                                        ttATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAGATGATGGCTATCTCACTCCAGTCAGAGCCACCAACTCAGGGCTGGAAAGTAAAAAACCGACGCAAAGTCGGTTTTTTTAc               >  1:698711/1‑139 (MQ=255)

                                                                                                                        ttATAAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAGATGATGGCTATCTCACTCCAGTCAGAGCCACCAACTCAGGGCTGGAAAGTAAAAAACCGACGCAAAGTCGGTTTTTTTAc               >  2:237026/1‑139 (MQ=255)

                                                                                                                        ttATAAAACCAGCACGCCCTTGCAATAGTTACAGTATGGTATTAGCATTGATGCGTTAGATGATGGCTATCTCACTCCAGTCAGAGCCACCAACTCAGGGCTGGAAAGTAAAAAACCGACGCAAAGTCGGTTTTTTTAc               >  1:115952/1‑139 (MQ=255)

                                                                                                                          ataAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAgat                                                                                             >  1:381136/1‑59 (MQ=255)

                                                                                                                          ataAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAgat                                                                                             <  2:381136/59‑1 (MQ=255)

                                                                                                                           taAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAGATGATGGCTATCTCACTCCAGTCAGAGCCACCAACTCAGGGCTGGAAAGTAAAAAACCGACGCAAAGTCGGTTTTTTTACATc            <  2:1093042/139‑1 (MQ=255)

                                                                                                                           taAAACCAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAGATGATGGCTATCTCACTCCAGTCAGAGCCACCAACTCAGGGCTGGAAAGTAAAAAACCGACGCAAAGTCGGTTTTTTTACATc            <  2:502643/139‑1 (MQ=255)

                                                                                                                                ccAGCACGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAGATGATGGCTATCTCACTCCAGTCAGAGCCACCAACTCAGGGCTGGAAAGTAAAAAACCGACGCAAAGTCGGTTTTTTTACATCCGGAt       <  2:782641/139‑1 (MQ=255)

                                                                                                                                     aCGCCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAGATGATGGCTATCTCACTCCAGTCAGAGCCACCAACTCAGGGCTGGAAAGTAAAAAACCGACGCAAAGTCGGTTTTTTTACATCCGGATTCGGa  <  2:837748/139‑1 (MQ=255)

GCCAGAGCATCAGTTAACGGCACCACCCGTACTTCTGACCAGGACTTTGAAAGCGTTTATGCGCATTGCCAGAGTGAAAATGCCTCAGAGCTAACTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGTCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAGATGATGGCTATCTCACTCCAGTCAGAGCCACCAACTCAGGGCTGGAAAGTAAAAAACCGACGCAAAGTCGGTTTTTTTACATCCGGATTCGGA  >  NC_000913/3647888‑3648159

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 28 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A