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
A1 F169 I0 R1	75	34.0	794130	95.7%	759982	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,657,158	C→T	38.9%	G174S (GGT→AGT)	comGA ←	ComG operon protein 1

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,657,158	0	C	T	38.9%	27.5 / 26.1	33	G174S (GGT→AGT)	comGA	ComG operon protein 1
Reads supporting (aligned to +/- strand): ref base C (9/11); new base T (6/7); total (15/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACTTGGCAACATCTTTATCTCTGATTTCACCTATTAAAATAACATCAGGATCACATCTTAAAATAGCTTTAAACGAATTTACATAGTTTATGCCAGCTTTATCATTCACATTAATTTGGACGATACCAGGAATTTGCATCTCTACAGGATCCTCTATAGAAATTACATTTAAATTCAAGGCTTTATTCGCGTATGAGACCATTTGATACATTAATGTACTCTTTCCTGAACCAGTTGGTCCACTAAACAATAGTAATCCTTGTT  >  USA300TCH1516_ALE/1657032‑1657295

acTTGGCAACATCTTTATCTCTGATTTCACCTATTAAAATAACATCAGGATCACATCTTAAAATAGCTTTAAACGAATTTACATAGTTTATGCCAGCTTTATCATTCACATTAATTTGGACGATACCAGGAATTTGCAtct                                                                                                                             >  1:216808/1‑141 (MQ=255)

     gCAACCTCTTTATCTCTGATTTCACCCATTAAAATCACATCAAGATCACATCTTAAAATAGCTTCAAACGAATTTACATAGTTTATGCCAGCTTTATCATTCACATTAATTTGGACGATACTCGGAATTTGCATCTCTACa                                                                                                                        <  2:359728/141‑1 (MQ=255)

     gCAACATCTTTATCTCTGATTTCACCTATTAAAATAACATCAGGATCACATCTTAAAATAGCTTTAAACGAATTTACATAGTTTATGCCAGCTTTATCATTCACATTAATTTGGACGATACTAGGAATTTGCATCTCTACa                                                                                                                        <  2:323335/141‑1 (MQ=255)

     gCAACATCTTTATCTCTGATTTCACCTATTAAAATAACATCAGGATCACATCTTAAAATAGCTTTAAACGAATTTACATAGTTTATGCCAGCTTTATCATTCACATTAATTTGGACGATACCAGGAATTTGCATCTCTACa                                                                                                                        <  2:290249/141‑1 (MQ=255)

      cAACATCTTTATCTCTGATTTCACCTATTAAAATAACATCAGGATCACATCTTAAAATAGCTTTAAACGAATTTACATAGTTTATGCCAGCTTTATCATTCACATTAATTTGGACGATACCAGGAATTTGCATCTCTACAg                                                                                                                       <  1:234230/141‑1 (MQ=255)

      cAACATCTTTATCTCTGATTTCACCTATTAAAATAACATCAGGATCACATCTTAAAATAGCTTTAAACGAATTTACATAGTTTATGCCAGCTTTATCATTCACATTAATTTGGACGATACCAGGAATTTGCATCTCGACAg                                                                                                                       <  2:145165/141‑1 (MQ=255)

              ttATCTCTGATTTCACCTATTAAAATAACATCAGGATCACATCTTAAAATAGCTTTAAACGAATTTACATAGTTTATGCCAGCTTTATCATTCACATTAATTTGGACGATACCAGGAATTTGCATCTCTACAGGATCctct                                                                                                               >  2:378051/1‑141 (MQ=255)

                  ctctGATTTCACCTATTAAAATAACATCAGGATCACATCTTAAAATAGCTTTAAACGAATTTACATAGTTTATGCCAGCTTTATCATTCACATTAATTTGGACGATACCAGGAATTTGCATCTCTACAGGATCCTCTATAg                                                                                                           <  1:381834/141‑1 (MQ=255)

                   tctGATTTCACCTATTAAAATAACATCAGGATCACATCTTAAAATAGCTTTAAACGAATTTACATAGTTTATGCCAGCTTTATCATTCACATTAATTTGGACGATACTAGGAATTTGCATCTCTACAGGATCCTCTATAGa                                                                                                          <  1:370672/141‑1 (MQ=255)

                      gATTTCACCTATTAAAATAACATCAGGATCACATCTTAAAATAGCTTTAAACGAATTTACATAGTTTATGCCAGCTTTATCATTCACATTAATTTGGACGATACTAGGAATTTGCATCTCTACAGGATCCTCTATAGAAAt                                                                                                       >  2:133902/1‑141 (MQ=255)

                            aCCTATTAAAATAACATCAGGATCACATCTTAAAATAGCTTTAAACGAATTTACATAGTTTATGCCAGCTTTATCATTCACATTAATTTGGACGATACTAGGAATTTGCATCTCTACAGGATCCTCTATAGAAATTACAtt                                                                                                 >  1:190421/1‑141 (MQ=255)

                            aCCTATTAAAATAACATCAGGATCACATCTTAAAATAGCTTTAAACGAATTTACATAGTTTATGCCAGCTTTATCATTCACATTAATTTGGACGATACCAGGAATTTGCATCTCTACAGGATCCTCTATAGAAATTACAtt                                                                                                 <  2:60742/141‑1 (MQ=255)

                            aCCTATTAAAATAACATCAGGATCACATCTTAAAATAGCTTTAAACGAATTTACATAGTTTATGCCAGCTTTATCATTCACATTAATTTGGACGATACCAGGAATTTGCATCTCTACAGGATCCTCTATAGAAATTACAtt                                                                                                 >  1:244043/1‑141 (MQ=255)

                                    aaaTAACATCAGGATCACATCTTAAAATAGCTTTAAACGAATTTACATAGTTTATGCCAGCTTTATCATTCACATTAATTTGGACGATACTAGGAATTTGCATCTCTACAGGATCCTCTATAGAAATTACATTTAAATTCa                                                                                         >  1:172156/1‑141 (MQ=255)

                                     aaTAACATCAGGATCACATCTTAAAATAGCTTTAAACGAATTTACATAGTTTATGCCAGCTTTATCATTCACATTAATTTGGACGGAACCTTATATTTGCATCTCTACAGGATCCTCTATAGAAATTACATTTAAATTCaa                                                                                        >  1:109890/1‑141 (MQ=255)

                                     aaTAACATCAGGATCACATCTTAAAATAGCTTTAAACGAATTTACATAGTTTATGCCAGCTTTATCATTCACATTAATTTGGACGATACTAGGAATTTGCATCTCTACAGGATCCTCTATAGAAATTACATTTAAATTCaa                                                                                        >  2:168277/1‑141 (MQ=255)

                                      aTAACATCAGGATCACATTTTAAAATAGCTTTAAACGAATTTACATAGTTTATGCCAGCTTTATCATTCACATTAATTTGGACGATACCAGGAATTTGCATCTCTACAGGATCCTCTATAGAAATTACATTTAAATTCAAg                                                                                       <  2:161710/141‑1 (MQ=255)

                                          cATCAGGATCACATCTTAAAATAGCTTTAAACGAATTTACATAGTTTATGCCAGCTTTATCATTCACATTAATTTGGACGATACCAGGAATTTGCATCTCTACAGGATCCTCTATAGAAATTACATTTAAATTCAAGGCtt                                                                                   <  1:248431/141‑1 (MQ=255)

                                               ggATCACATCTTAAAATAGCTTTAAACGAATTTACATAGTTTATGCCAGCTTTATCATTCACATTAATTTGGACGATACTAGGAATTTGCATCTCTACAGGATCCTCTATAGAAATTACATTTAAATTCAAGGCTTTATTc                                                                              <  1:218324/141‑1 (MQ=255)

                                                        cTTAAAATAGCTTTAAACGAATTTACATAGTTTATGCCAGCTTTATCATTCACATTAATTTGGACGATACCAGGAATTTGCATCTCTACAGGATCCTCTATAGAAATTACATTTAAATTCAAGGCTTTATTCGCGTATgag                                                                     <  2:216808/141‑1 (MQ=255)

                                                               tAGCTTTAAACGAATTTACATAGTTTATGCCAGCTTTATCATTCACATTAATTTGGACGATACCAGGAATTTGCATCTCTACAGGATCCTCTATAGAAATTACATTTAAATTCAAGGCTTTATTCGCGTATGAGACCAttt                                                              >  2:345265/1‑141 (MQ=255)

                                                                    ttAAACGAATTTACATAGTTTATGCCAGCTTTATCATTCACATTAATTTGGACGATACTAGGAATTTGCATCTCTACAGGATCCTCTATAGAAATTACATTTAAATTCAAGGCTTTATTCGCGTATGAGACCATTTGATAc                                                         >  1:369724/1‑141 (MQ=255)

                                                                    ttAAACGAATTTACATAGTTTATGCCAGCTTTATCATTCACATTAATTTGGACGATACCAGGAATTTGCATCTCTACAGGATCCTCTATAGAAATTACATTTAAATTCAAGGCTTTATTCGCGTATGAGACCATTTGATAc                                                         <  2:244043/141‑1 (MQ=255)

                                                                                   tAGTTTATGCCAGCTTTATCATTCACATTAATTTGGACGATACCAGGAATTTGCATCTCTACAGGATCCTCTATAGAAATTACATTTAAATCCAAGGCTTTATTCGCGTATGAGACCATTTGATACATTAATGTACTCttt                                          >  1:171073/1‑141 (MQ=255)

                                                                                           gCCAGCTTTATCATTCACATTAATTTGGACGATACCAGGAATTTGCATCTCTACAGGATCCTCTATAGAAATTACATTTAAATTCAAGGCTTTATTCGCGTATGAGACCATTTGATACATTAATGTACTCTTTCCTGAAcc                                  >  1:125616/1‑141 (MQ=255)

                                                                                              aGCTTTATCATTCACATTAATTTGGACGATACTAGGAATTTGCATCTCTACAGGATCCTCTATAGAAATTACATTTAAATTCAAGGCTTTATTCGCGTATGAGACCATTTGATACATTAATGTACTCTTTCCTGAACCAGt                               >  1:77350/1‑141 (MQ=255)

                                                                                              aGCTTTATCATTCACATTAATTTGGACGATACCAGGAATTTGCATCTCTACAGGATCCTCTATAGAAATTACATTTAAATTCAAGGCTTTATTCGCGTATGAGACCATTTGATACATTAATGTACTCTTTCCTGAACCAGt                               >  2:178637/1‑141 (MQ=255)

                                                                                               gCTTTATCATTCACATTAATTTGGACGATACCAGGAATTTGCATCTCTACAGGATCCTCTATAGAAATTACATTTAAATTCAAGGCTTTATTCGCGTATGAGACCATTTGATACATTAATGTACTCTTTCCTGAACCAGtt                              <  2:12753/141‑1 (MQ=255)

                                                                                                      cATTCACATTAATTTGGACGATACTAGGAATTTGCATCTCTACAGGATCCTCTATAGAAATTACATTTAAATTCAAGGCTTTATTCGCGTATGAGACCATTTGATACATTAATGTACTCTTTCCTGAACCAGTTGGTCCAc                       <  2:172156/141‑1 (MQ=255)

                                                                                                      cATTCACATTAATTTGGACGATACCAGGAATTTGCATCTCTACAGGATCCTCTATAGAAATTACATTTAAATTCAAGGCTTTATTCGCGTATGAGACCATTTGATACATTAATGTACTCTTTCCTGAACCAGTTGGTCCAc                       <  2:147941/141‑1 (MQ=255)

                                                                                                       aTTCACATGAATTTGGACGATACTAGGAATTTGCATCTCTACAGGATCCTCTATAGAAATTACATTTAAATTCAAGGCTTTATTCGCGTATGAGACCATTTGATACATTAATGTACTCTTTCCTGAACCAGTTGGTCCACt                      <  2:19165/141‑1 (MQ=255)

                                                                                                             aTTAATTTGGACGATACCAGGAATTTGCATCTCTACAGGATCCTCTATAGAAATTACATTTAAATTCAAGGCTTTATTCGCGTATGAGACCATTTGATACATTAATGTACTCTTTCCTGAACCAGTTGGTCCACTAAACaa                >  2:201475/1‑141 (MQ=255)

                                                                                                                           tACTAGGAATTTGCATCTCTACAGGATCCTATCTTGAAATTACATTTCAATTCAAGACTTTATTCGCGTATTAGACCATTTGATACATTACTGTACTCTTTCCTGAACCAGTTGGTCCACTAAACAATAGTAATCCTTGtt  <  2:190421/141‑1 (MQ=255)

ACTTGGCAACATCTTTATCTCTGATTTCACCTATTAAAATAACATCAGGATCACATCTTAAAATAGCTTTAAACGAATTTACATAGTTTATGCCAGCTTTATCATTCACATTAATTTGGACGATACCAGGAATTTGCATCTCTACAGGATCCTCTATAGAAATTACATTTAAATTCAAGGCTTTATTCGCGTATGAGACCATTTGATACATTAATGTACTCTTTCCTGAACCAGTTGGTCCACTAAACAATAGTAATCCTTGTT  >  USA300TCH1516_ALE/1657032‑1657295

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