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
A7 F28 I1 R1	183	98.6	3427438	96.9%	3321187	138.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,119,166	T→C	intergenic (‑54/+431)	yghJ ← / ← glcA	putative lipoprotein YghJ/glycolate/lactate:H(+) symporter GlcA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,119,166	0	T	C	98.3%	213.0 / ‑4.3	59	intergenic (‑54/+431)	yghJ/glcA	putative lipoprotein YghJ/glycolate/lactate:H(+) symporter GlcA
Reads supporting (aligned to +/- strand): ref base T (1/0); new base C (28/30); total (29/30)
Fisher's exact test for biased strand distribution p-value = 4.92e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.63e-01

CCACCGCCATCACAACCGGCTAACAGGGTTGCGCTCAAAATAGCCGCTAAAAGCGATTTCTTATATTTAAATTTCTTATTCATTAATAACGCAAGTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGTTTTATGCTTTATCTTCTCTAATAACTTCCTCCATTCTTAAGAAAACGACATCATTGATAGAAAACAGGTGAAATTTATAAGAATAACCCCTATACGATGTCTATCTGGCTATTTTTACGAAATTTCAACAAACAAA  >  NC_000913/3119030‑3119302

ccaccGCCATCACAACCGGCTAACAGGGTTGCGCTCAAAATAGCCGCTAAAAGCGATTTCTTATATTTAAATTTCTTATTCATTAATAACGCAAGTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGcttt                                                                                                                                       <  2:583059/140‑1 (MQ=255)

   ccGCCATCACAACCGGCTAACAGGGTTGCGCTCAAAATAGCCGCTAAAAGCGATTTCTTATATTTAAATTTCTTATTCATTAATAACGCAAGTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATg                                                                                                                                    >  2:780007/1‑140 (MQ=255)

           acaACCGGCTAACAGGGTTGCGCTCAAAATAGCCGCTAAAAGCGATTTCTTATATTTAAATTTCTTATTCATTAATAACGCAAGTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTAtct                                                                                                                            <  2:1251072/140‑1 (MQ=255)

            caACCGGCTAACAGGGTTGCGCTCAAAATAGCCGCTAAAAGCGATTTCTTATATTTAAATTTCTTATTCATTAATAACGCAAGTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTAtctt                                                                                                                           <  2:1421701/140‑1 (MQ=255)

                 ggCTAACAGGGTTGCGCTCAAAATAGCCGCTAAAAGCGATTTCTTATATTTAAATTTCTTATTCATTAATAACGCAAGTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCta                                                                                                                      <  2:264737/140‑1 (MQ=255)

                  gCTAACAGGGTTGCGCTCAAAATAGCCGCTAAAAGCGATTTCTTATATTTAAATTTCTTATTCATTAATAACGCAAGTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCtaa                                                                                                                     <  1:261410/140‑1 (MQ=255)

                      aCAGGGTTGCGCTCAAAATAGCCGCTAAAAGCGATTTCTTATATTTAAATTTCTTATTCATTAATAACGCAAGTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAAc                                                                                                                 <  2:384841/140‑1 (MQ=255)

                       cAGGGTTGCGCTCAAAATAGCCGCTAAAAGCGATTTCTTATATTTAAATTTCTTATTCATTAATAACGCAAGTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAACt                                                                                                                <  2:331445/140‑1 (MQ=255)

                           gTTGCGCTCAAAATAGCCGCTAAAAGCGATTTCTTATATTTAAATTTCTTATTCATTAATAACGCAAGTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTAtc                                                                                                                             >  1:863484/1‑123 (MQ=255)

                           gTTGCGCTCAAAATAGCCGCTAAAAGCGATTTCTTATATTTAAATTTCTTATTCATTAATAACGCAAGTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTAtc                                                                                                                             <  2:863484/123‑1 (MQ=255)

                           gTTGCGCTCAAAATAGCCGCTAAAAGCGATTTCTTATATTTAAATTTCTTATTCATTAATAACGCAAGTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTtcct                                                                                                            <  2:927529/140‑1 (MQ=255)

                           gTTGCGCTCAAAATAGCCGCTAAAAGCGATTTCTTATATTTAAATTTCTTATTCATTAATAACGCAAGTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTtcct                                                                                                            <  1:19523/140‑1 (MQ=255)

                             tGCGCTCAAAATAGCCGCTAAAAGCGATTTCTTATATTTAAATTTCTTATTCATTAATAACGCAAGTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTtcctcc                                                                                                          >  1:728112/1‑140 (MQ=255)

                               cgcTCAAAATAGCCGCTAAAAGCGATTTCTTATATTTAAATTTCTTATTCATTAATAACGCAAGTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTTCCTCCAt                                                                                                        >  2:150851/1‑140 (MQ=255)

                               cgcTCAAAATAGCCGCTAAAAGCGATTTCTTATATTTAAATTTCTTATTCATTAATAACGCAAGTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTTCCTCCAt                                                                                                        >  1:795532/1‑140 (MQ=255)

                                 cTCAAAATAGCCGCTAAAAGCGATTTCTTATATTTAAATTTCTTATTCATTAATAACGCAAGTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTtcct                                                                                                            <  2:677326/134‑1 (MQ=255)

                                 cTCAAAATAGCCGCTAAAAGCGATTTCTTATATTTAAATTTCTTATTCATTAATAACGCAAGTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTtcct                                                                                                            >  1:677326/1‑134 (MQ=255)

                                 cTCAAAATAGCCGCTAAAAGCGATTTCTTATATTTAAATTTCTTATTCATTAATAACGCAAGTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTTCCTCCATTc                                                                                                      >  2:744223/1‑140 (MQ=255)

                                   cAAAATAGCCGCTAAAAGCGATTTCTTATATTTAAATTTCTTATTCATTAATAACGCAAGTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTTCCTCCATTCtt                                                                                                    <  1:150851/140‑1 (MQ=255)

                                      aaTAGCCGCTAAAAGCGATTTCTTATATTTAAATTTCTTATTCATTAATAACGCAAGTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTTCCTCCATTCTTAAg                                                                                                 >  1:859441/1‑140 (MQ=255)

                                        tAGCCGCTAAAAGCGATTTCTTATATTTAAATTTCTTATTCATTAATAACGCAAGTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTTCCTCCATTCTTAAGaa                                                                                               <  1:744223/140‑1 (MQ=255)

                                                aaaaGCGATTTCTTATATTTAAATTTCTTATTCATTAATAACGCAAGTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGTTTTATGCTTTATCTTCTCTAATAACTTCCTCCATTCTTAAGAAAACGAcat                                                                                       >  2:1069445/1‑140 (MQ=255)

                                                   aGCGATTTCTTATATTTAAATTTCTTATTCATTAATAACGCAAGTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTTCCTCCATTCTTAAGAAAACGAcatcat                                                                                    <  1:576695/140‑1 (MQ=255)

                                                                   tAAATTTCTTATTCATTAATAACGCAAGTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTTCCTCCATTCTTAAGAAAACGACATCATTGATAGAAAACAGGTg                                                                    <  1:1426392/140‑1 (MQ=255)

                                                                   tAAATTTCTTATTCATTAATAACGCAAGTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTTCCTCCATTCTTAAGAAAACGACATCATTGATAGAAAACAGGTg                                                                    <  1:1524229/140‑1 (MQ=255)

                                                                          cTTATTCATTAATAACGCAAGTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTTCCTCCATTCTTAAGAAAACGACATCATTGATAGAAAACAGGTGAAATTta                                                             >  1:1522776/1‑140 (MQ=255)

                                                                                  ttAATAACGCAAGTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTTCCTCCATTCTTAAGAAAACGACATCATTGATAGAAAACAGGTGAAATTTATAAGAATa                                                     >  2:960438/1‑140 (MQ=255)

                                                                                   taataaCGCAAGTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTTCCTCCATTCTTAAGAAAACGACATCATTGATAGAAAACAGGTGAAATTTATAAGAATaa                                                    <  2:795532/140‑1 (MQ=255)

                                                                                   taataaCGCAAGTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTTCCTCCATTCTTAAGAAAACGACATCATTGATAGAAAACAGGTGAAATTTATAAGAATaa                                                    >  2:331456/1‑140 (MQ=255)

                                                                                   taataaCGCAAGTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTTCCTCCATTCTTAAGAAAACGACATCATTGATAGAAAACAGGTGAAATTTATAAGAATaa                                                    <  2:859441/140‑1 (MQ=255)

                                                                                   taataaCGCAAGTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTTCCTCCATTCTTAAGAAAACGACATCATTGATAGAAAACAGGTGAAATTTATAAGAATaa                                                    <  1:1709843/140‑1 (MQ=255)

                                                                                        aCGCAAGTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTTCCTCCATTCTTAAGAAAACGACATCATTGATAGAAAACAGGTGAAATTTATAAGAAt                                                      >  2:303980/1‑133 (MQ=255)

                                                                                        aCGCAAGTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTTCCTCCATTCTTAAGAAAACGACATCATTGATAGAAAACAGGTGAAATTTATAAGAAt                                                      <  1:303980/133‑1 (MQ=255)

                                                                                         cGCAAGTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTTCCTCCATTCTTAAGAAAACGACATCATTGATAGAAAACAGGTGAAATTtat                                                            >  2:122744/1‑126 (MQ=255)

                                                                                         cGCAAGTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTTCCTCCATTCTTAAGAAAACGACATCATTGATAGAAAACAGGTGAAATTtat                                                            <  1:122744/126‑1 (MQ=255)

                                                                                           cAAGTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTTCCTCCATTCTTAAGAAAACGACATCATTGATAGAAAACAGGTGAAATTTATAAGAAt                                                      <  2:303981/130‑1 (MQ=255)

                                                                                           cAAGTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTTCCTCCATTCTTAAGAAAACGACATCATTGATAGAAAACAGGTGAAATTTATAAGAAt                                                      >  1:303981/1‑130 (MQ=255)

                                                                                           cAAGTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTTCCTCCATTCTTAAGAAAACGACATCATTGATAGAAAACAGGTGAAATTTATAAGAATAACCCCtata                                            >  2:1388894/1‑140 (MQ=255)

                                                                                           cAAGTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTTCCTCCATTCTTAAGAAAACGACATCATTGATAGAAAACAGGTGAAATTTATAAGAATAACCCCtata                                            <  1:960438/140‑1 (MQ=255)

                                                                                             aGTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTTCCTCCATTCTTAAGAAAACGACATCATTGATAGAAAACAGGTGAAATTTATAAGAATAACCCCTATACg                                          <  1:780007/140‑1 (MQ=255)

                                                                                              gTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTTCCTCCATTCTTAAGAAAACGACATCATTGATAGAAAACAGGTGAAATTTATAAGAATAACCCCtata                                            >  2:664961/1‑137 (MQ=255)

                                                                                              gTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTTCCTCCATTCTTAAGAAAACGACATCATTGATAGAAAACAGGTGAAATTTATAAGAATAACCCCtata                                            <  1:664961/137‑1 (MQ=255)

                                                                                              gTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTTCCTCCATTCTTAAGAAAACGACATCATTGATAGAAAACAGGTGAAATTTATAAGAATAACCCCTATACGa                                         >  2:1408051/1‑140 (MQ=255)

                                                                                              gTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTTCCTCCATTCTTAAGAAAACGACATCATTGATAGAAAACAGGTGAAATTTATAAGAATAACCCCTATACGa                                         >  1:101115/1‑140 (MQ=255)

                                                                                               tGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTTCCTCCATTCTTAAGAAAACGACATCATTGATAGAAAACAGGTGAAATTTATAAGAATAACCCCTATACGAt                                        >  2:1096270/1‑140 (MQ=255)

                                                                                               tGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTTCCTCCATTCTTAAGAAAACGACATCATTGATAGAAAACAGGTGAAATTTATAAGAATAACCCCTATACGAt                                        <  2:101115/140‑1 (MQ=255)

                                                                                                 aCAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTTCCTCCATTCTTAAGAAAACGACATCATTGATAGAAAACAGGTGAAATTTATAAGAATAACCCCTATACGATGt                                      <  2:1522776/140‑1 (MQ=255)

                                                                                                   aaaaCAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTTCCTCCATTCTTAAGAAAACGACATCATTGATAGAAAACAGGTGAAATTTATAAGAATAACCCCTATACGATGTCt                                    >  2:1098320/1‑140 (MQ=255)

                                                                                                     aaCAATGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTTCCTCCATTCTTAAGAAAACGACATCATTGATAGAAAACAGGTGAAATTTATAAGAATAACCCCTATACGATGTCTAt                                  <  1:1707671/140‑1 (MQ=255)

                                                                                                        aaTGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTTCCTCCATTCTTAAGAAAACGACATCATTGATAGAAAACAGGTGAAATTTATAAGAATAACCCCTATACGATGTCTATCTg                               >  2:1157110/1‑140 (MQ=255)

                                                                                                          tGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTTCCTCCATTCTTAAGAAAACGACATCATTGATAGAAAACAGGTGAAATTTATAAGAATAACCCCtata                                            <  2:1015594/125‑1 (MQ=255)

                                                                                                          tGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTTCCTCCATTCTTAAGAAAACGACATCATTGATAGAAAACAGGTGAAATTTATAAGAATAACCCCtata                                            >  1:1015594/1‑125 (MQ=255)

                                                                                                          tGTTAAAAAATTCGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTTCCTCCATTCTTAAGAAAACGACATCATTGATAGAAAACAGGTGAAATTTATAAGAATAACCCCTATACGATGTCTATCTGGc                             >  1:868375/1‑140 (MQ=255)

                                                                                                                      cGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTTCCTCCATTCTTAAGAAAACGACATCATTGATAGAAAACAGGTGAAATTTATAAGAATAACCCCTATACGATGTCTATCTGGCTATTTTTACGaa                 >  2:195140/1‑140 (MQ=255)

                                                                                                                      cGTAACTGGGAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTTCCTCCATTCTTAAGAAAACGACATCATTGATAGAAAACAGGTGAAATTTATAAGAATAACCCCTATACGATGTCTATCTGGCTATTTTTACGaa                 >  1:546249/1‑140 (MQ=255)

                                                                                                                              ggAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTTCCTCCATTCTTAAGAAAACGACATCATTGATAGAAAACAGGTGAAATTTATAAGAATAACCCCTATACGATGTCTATCTGGCTATTTTTACGAAATTTcaac         >  1:816738/1‑140 (MQ=255)

                                                                                                                              ggAGAAATAGCTTTATGCTTTATCTTCTCTAATAACTTCCTCCATTCTTAAGAAAACGACATCATTGATAGAAAACAGGTGAAATTTATAAGAATAACCCCTATACGATGTCTATCTGGCTATTTTTACGAAATTTcaac         >  1:784459/1‑140 (MQ=255)

                                                                                                                               gagaAATAGCTTTATGCTTTATCTTCTCTAATAACTTCCTCCATTCTTAAGAAAACGACATCATTGATAGAAAACAGGTGAAATTTATAAGAATAACCCCTATACGATGTCTATCTGGCTATTTTTACGAAATTTcaaca        >  2:1397651/1‑140 (MQ=255)

                                                                                                                                     tAGCTTTATGCTTTATCTTCTCTAATAACTTCCTCCATTCTTAAGAAAACGACATCATTGATAGAAAACAGGTGAAATTTATAAGAATAACCCCTATACGATGTCTATCTGGCTATTTTTACGAAATTTcaa          <  1:1633196/132‑1 (MQ=255)

                                                                                                                                     tAGCTTTATGCTTTATCTTCTCTAATAACTTCCTCCATTCTTAAGAAAACGACATCATTGATAGAAAACAGGTGAAATTTATAAGAATAACCCCTATACGATGTCTATCTGGCTATTTTTACGAAATTTCAAcaaacaaa  <  1:1408051/140‑1 (MQ=255)

CCACCGCCATCACAACCGGCTAACAGGGTTGCGCTCAAAATAGCCGCTAAAAGCGATTTCTTATATTTAAATTTCTTATTCATTAATAACGCAAGTGACAAAACAATGTTAAAAAATTCGTAACTGGGAGAAATAGTTTTATGCTTTATCTTCTCTAATAACTTCCTCCATTCTTAAGAAAACGACATCATTGATAGAAAACAGGTGAAATTTATAAGAATAACCCCTATACGATGTCTATCTGGCTATTTTTACGAAATTTCAACAAACAAA  >  NC_000913/3119030‑3119302

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A