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
A5 F58 I0 R1	54	56.9	1222162	95.8%	1170831	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,196,508	C→A	83.8%	intergenic (+2563/‑1229)	ftsQ → / → USA300HOU_1125	cell division protein FtsQ/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,196,508	0	C	A	83.8%	124.7 / 20.2	62	intergenic (+2563/‑1229)	ftsQ/USA300HOU_1125	cell division protein FtsQ/hypothetical protein
Reads supporting (aligned to +/- strand): ref base C (4/6); new base A (24/28); total (28/34)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.00e-01

CGGTACAGTTATTAATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTCTAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCTTCATTAGAAATAGAGAAGAAA  >  CP000730/1196377‑1196642

cGGTACAGTTATTAATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTCAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTCTAGCAATGc                                                                                                                               <  1:419457/141‑1 (MQ=255)

cGGTACAGTTATTAATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGc                                                                                                                               >  2:393530/1‑141 (MQ=255)

 ggTACAGTTATTAATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAACCGTAAATACTTATAGCAATGCa                                                                                                                              >  1:576322/1‑141 (MQ=255)

   tACAGTTATTAATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTCTAGCAATGCAAc                                                                                                                            <  1:339431/141‑1 (MQ=255)

    aCAGTTATTAATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTCTAGCAATGCAACt                                                                                                                           <  1:100281/141‑1 (MQ=255)

        ttattaATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTCAAAAACAAACTTATTTCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTa                                                                                                                       <  1:141213/141‑1 (MQ=255)

              aTCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATg                                                                                                                 <  2:471919/141‑1 (MQ=255)

                 cggAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAAt                                                                                                              <  1:553874/139‑1 (MQ=255)

                     aTTACAAGATGAGGTTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCAtt                                                                                                          <  2:610167/141‑1 (MQ=255)

                     aTTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCAtt                                                                                                          >  2:317619/1‑141 (MQ=255)

                      ttccAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTc                                                                                                         <  1:276063/138‑1 (MQ=255)

                        aCAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTCTAGCAATGCAACTTCTAAAGATGAATCATTCAc                                                                                                       >  1:187840/1‑141 (MQ=255)

                        aCAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCAc                                                                                                       >  2:544030/1‑141 (MQ=255)

                         aaaGATGAGATTGTTGTAACAGTGATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCCTTcgtt                                                                                                      <  2:158471/140‑4 (MQ=255)

                           aGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTc                                                                                                    >  1:378608/1‑141 (MQ=255)

                             aTGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCaa                                                                                                  >  2:589828/1‑141 (MQ=255)

                             aTGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACCGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAATGATAAATCATTCACTTCaa                                                                                                  <  1:455621/141‑1 (MQ=255)

                               gagaTTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAAt                                                                                                <  1:568537/141‑1 (MQ=255)

                                 gaTTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATtc                                                                                              <  1:84079/141‑1 (MQ=255)

                                  aTTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATtca                                                                                             <  2:1353/141‑1 (MQ=255)

                                       tgtAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCaaa                                                                                        >  2:600763/1‑141 (MQ=255)

                                        gtAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATtcatca                                                                                          >  1:511145/1‑138 (MQ=255)

                                        gtAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATtcatca                                                                                          <  2:511145/138‑1 (MQ=255)

                                          aaCAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGAAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGc                                                                                     <  1:117903/141‑1 (MQ=255)

                                               ttATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAACTTCATCAAATGCACAAg                                                                                >  2:305344/1‑141 (MQ=255)

                                                  ttGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACACGCaa                                                                             <  1:417160/141‑1 (MQ=255)

                                                    gCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACt                                                                           >  2:560756/1‑141 (MQ=255)

                                                    gCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTAGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACt                                                                           >  2:341295/1‑141 (MQ=255)

                                                      aaCTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGa                                                                         >  1:493443/1‑141 (MQ=255)

                                                       aCTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGAt                                                                        <  2:235209/141‑1 (MQ=255)

                                                          ggTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTTAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGACAgt                                                                     >  2:400368/1‑141 (MQ=255)

                                                             tttGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTCTAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTa                                                                  >  2:566931/1‑141 (MQ=255)

                                                                 gggaCAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTg                                                              <  1:64668/139‑1 (MQ=255)

                                                                       acccAACATCACATGTTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGaa                                                        <  2:120873/139‑1 (MQ=255)

                                                                       aaCCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGCTAGTGTAAGTGAAAGaa                                                        >  2:331675/1‑141 (MQ=255)

                                                                       aaCCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGaa                                                        <  1:128172/141‑1 (MQ=255)

                                                                         ccAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAaca                                                      <  2:121211/141‑1 (MQ=255)

                                                                          cAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAacac                                                     <  1:289790/141‑1 (MQ=255)

                                                                           aaCATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAAcaca                                                    >  1:458768/1‑141 (MQ=255)

                                                                           aaCATCACATGGTCGTAAATCTGGTAGCACTGGATTCAGAACAAGCGTAAATACTTCTAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAATGTAAGTGAAAGAGcaca                                                    >  1:242376/1‑141 (MQ=255)

                                                                            aCATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGGATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACCCAt                                                   >  1:141890/1‑141 (MQ=255)

                                                                               tCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTCTAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACa                                                >  1:504189/1‑141 (MQ=255)

                                                                               tCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACa                                                >  1:71411/1‑141 (MQ=255)

                                                                                 acaTGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTCTAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAAc                                              <  2:487969/141‑1 (MQ=255)

                                                                                  cctGGTCCTAAATCGGGTAGCACTGAGTTCGGAACAAGCGTAAATCCTTATAGGAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACt                                             <  2:269892/139‑1 (MQ=255)

                                                                                  caTGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACt                                             <  2:423175/141‑1 (MQ=255)

                                                                                  caTGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACt                                             <  1:459718/141‑1 (MQ=255)

                                                                                         gTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTGCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAaagaag                                      >  1:115534/1‑141 (MQ=255)

                                                                                           aaaTCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAgat                                    <  2:43625/141‑1 (MQ=255)

                                                                                               cTGGTAGCACTGGATTCGGAACAAGCGGAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGataata                                >  2:9722/1‑141 (MQ=255)

                                                                                                   tAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTcc                            >  2:130030/1‑141 (MQ=255)

                                                                                                     gCACTGGATTCGGAACAAGCGTAAATACTTCTAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTa                          <  1:566931/141‑1 (MQ=255)

                                                                                                     gCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGAACAAGAAACCGGTAGGGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTa                          >  1:17266/1‑141 (MQ=255)

                                                                                                      cACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAg                         <  2:71411/141‑1 (MQ=255)

                                                                                                         tGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTTCAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCtt                      <  2:211368/141‑1 (MQ=255)

                                                                                                          ggATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCTTc                     <  2:135179/141‑1 (MQ=255)

                                                                                                              tCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTCAAGAAGATGATATTCCTAGCTTCATTa                 >  2:518184/1‑141 (MQ=255)

                                                                                                                    cAAGCGTAAATACTTCTAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCTTCATTAGAAATa           <  1:69708/141‑1 (MQ=255)

                                                                                                                    cAAGCGTAAATACTGATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCTTCATTAGAAATa           <  2:157638/141‑1 (MQ=255)

                                                                                                                       gCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCTTCATTAGAAATagag        >  1:521535/1‑141 (MQ=255)

                                                                                                                          tAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCTTCATTAGACATAGagaag     >  2:424215/1‑141 (MQ=255)

                                                                                                                             aTACTTATAGCAATGCAACTTCTAAAGATGAATCATTAAAGACAAATGCAGCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCTTCATTAGAAATAGAGaagaaa  <  1:317619/141‑1 (MQ=255)

CGGTACAGTTATTAATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTCTAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCTTCATTAGAAATAGAGAAGAAA  >  CP000730/1196377‑1196642

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A