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 I1 R1	59	38.6	831760	90.8%	755238	148.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	51,334	(G)_7→8	coding (36/1092 nt)	USA300HOU_0043 →	hypothetical membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	51,327	1	.	G	97.7%	144.9 / ‑1.7	43	coding (29/1092 nt)	USA300HOU_0043	hypothetical membrane protein
Reads supporting (aligned to +/- strand): ref base . (1/0); new base G (27/15); total (28/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.05e-01

TGCTGCTTAGATTTCTTATTCATTTTAAAATTCCTCCAATAATTTTTAAGGAGTCAATCAATATCATATAGGTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGA‑GGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAGGTTTATGAAGATTTGTTGTTATTAAGAAGTTTAAGCGATTTAAATGAA  >  CP000730/51180‑51466

tgctgcTTAGATTTCTTATTCATTTTAAAATTCCTCCAATAATTTTTAAGGAGTCAATCAATATCATATAGGTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGa                                                                                                                                              >  2:371691/1‑148 (MQ=255)

   tgctTAGATTTCTTATTCATTTTAAAATTCCTCCAATAATTTTTAAGGAGTCAATCAATATCATATAGGTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGA‑ggg                                                                                                                                          <  1:60543/148‑1 (MQ=255)

      ttAGATTTCTTATTCATTTTAAAATTCCTCCAATAATTTTTAAGGAGTCAATCAATATCATATAGGTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAAAAAAAAATGGGGA‑gggggg                                                                                                                                       <  2:163450/148‑1 (MQ=255)

      ttAGATTTCTTATTAATTTAAAAAATCCTCAAAAAATTTTTAAGGGGTCAATAAATATCAAAAAGGTTAAACTATCTTCAATTGATTGCTATAAAAAGCATAAATGAAGCATTATGTTAAAAAAAAAAAAAAAAAATGGGGA‑gggggg                                                                                                                                       <  2:180840/148‑1 (MQ=255)

        aGATTTCTTATTCATTTTAAAATTCCTCCAATAATTTTTAAGGAGTCAATCAATATCATATAGGTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGA‑gggggggg                                                                                                                                     <  1:60274/148‑2 (MQ=255)

           tttCTTATTCATTTTAAAATTCCTCCAATAATTTTTAAGTAGTCAATCAATATCATATAGGTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGA‑ggggggggtat                                                                                                                                  >  1:201893/1‑144 (MQ=255)

           tttCTTATTCATTTTAAAATTCCTCCAATAATTTTTAAGGAGTCAATCAATATCATATAGGTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGA‑ggggggagtat                                                                                                                                  >  2:356976/1‑143 (MQ=255)

               ttATTCATTTTAAAATTCCTCCAATAATTTTTAAGGAGTCAATCAATATCATATAGGTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTatatat                                                                                                                               >  1:89296/1‑148 (MQ=255)

                   tCATTTTAATATTCCTTCAATAATTTTTAAGGAGTCAATCAATATCATATAGGTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGAt                                                                                                                           <  2:404274/148‑1 (MQ=255)

                      ttttAAAATTCCTCCAATAATTTTTAAGGAGTCAATCAATATCATATAGGTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTTTATATTGATAcc                                                                                                                        >  2:19175/1‑148 (MQ=255)

                      ttttAAAATTCCTCCAATAATTTTTAAGGAGTCAATCAATATCATATAGGTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATAcc                                                                                                                        >  1:132458/1‑148 (MQ=255)

                                    cAATAATTTTTAAGGAGTAAATAAATATCATATAGGTTAAACTAGCTTCAATTGATTGCTATAATAAGCATAAAGGAAGCATTATGATTAGAAAAAAAAAAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGaaa                                                                                                          <  2:236207/148‑1 (MQ=255)

                                       taatTTTTAAGGAGTCAATCAATATCATATAGGTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGA‑GGGGGGGTATATATTGATACCTACGCTAGAAGAAattat                                                                                                      >  1:250354/1‑148 (MQ=255)

                                         atTTTTAAGGAGTCAATCAATATCATATAGGTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAattatt                                                                                                     >  2:242749/1‑148 (MQ=255)

                                                       aatcactAACATATGAATTAAATAATCTTAACGTGAAAGCTAAAATAAGCAAAAATGAAGAATTATGATTAGACCTGAAACAAAAAATGAGGAGGGGGGGGTATATACTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGaag                                                                                       <  2:268378/148‑2 (MQ=255)

                                                                       gTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTg                                                                       >  1:249390/1‑148 (MQ=255)

                                                                        ttAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGa                                                                      >  1:272631/1‑148 (MQ=255)

                                                                        ttAAACTAACTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGa                                                                      <  2:8298/148‑1 (MQ=255)

                                                                         tAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTCTGATTCTTCGCGGAAGGAAAAATGGGGAGGGGGGGGGATAAATTGATACATACGCTAGACGAACTTATTGATAAGTATGGAAACTTAGTTGATAATTTGaa                                                                     >  2:408010/1‑148 (MQ=255)

                                                                         tAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGaa                                                                     >  1:61888/1‑148 (MQ=255)

                                                                         tAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGAGTATACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGaa                                                                     >  1:303742/1‑148 (MQ=255)

                                                                         tAAACTATCATCAACGTATTGCTATAATAAGCCTAAATGAAGCGTTATGCTTAGACGCGGAACTAGAAATGGGGAGGGGGGGGAATATATTGATACCTACGCTAGCATAACTTATTGATGAGTATGTACCCTTAGCTGAATATTTgca                                                                     >  2:408044/1‑146 (MQ=255)

                                                                             cTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAAttt                                                                 >  1:257145/1‑148 (MQ=255)

                                                                                  ttCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGt                                                            <  2:79932/148‑1 (MQ=255)

                                                                                  ttCAATTGATTGATATAATAAGCATAAAGGAAGCATTATGATTAAAAGAAGAAAAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGt                                                            <  2:381542/148‑1 (MQ=255)

                                                                                  tgcaatcggatggcataataAGCTTAAGTGGTGTATTATTATTAAAAAAAAAAAAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGt                                                            <  2:163620/134‑1 (MQ=255)

                                                                                       ttgattgCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAg                                                       >  1:20255/1‑148 (MQ=255)

                                                                                       ttgattgCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGGATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGACTATTTGAAATTTGATGTAACAg                                                       >  2:307536/1‑148 (MQ=255)

                                                                                        tgattgCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGt                                                      >  1:318777/1‑148 (MQ=255)

                                                                                            tgCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAg                                                  >  1:234398/1‑148 (MQ=255)

                                                                                            tgCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAg                                                  >  2:154521/1‑148 (MQ=255)

                                                                                             acTATAATAAGAATAAATGAAGCATTATGATTAGAAAAAAAAAAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAgg                                                 <  2:205350/147‑1 (MQ=255)

                                                                                               tataATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAGGtt                                               >  1:368999/1‑148 (MQ=255)

                                                                                               tataATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAGGtt                                               >  1:295161/1‑148 (MQ=255)

                                                                                               tataATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATGATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGCTGTAACAGTTGAGGtt                                               >  1:369008/1‑148 (MQ=255)

                                                                                                ataataAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAGGttt                                              <  2:28868/148‑1 (MQ=255)

                                                                                                ataataAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAGGttt                                              <  2:28797/148‑1 (MQ=255)

                                                                                                 taataaGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAGGTTTa                                             >  2:46456/1‑148 (MQ=255)

                                                                                                 taataaGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGCATATATTGATACCTACGCGAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGAGTATTTGAAATTTGATGTAACAGTTGAGGTTTa                                             >  2:178030/1‑148 (MQ=255)

                                                                                                              tGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAGGTTTATGAAGATttgttg                                >  1:165833/1‑148 (MQ=255)

                                                                                                               gAAGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAGGTTTATGAAGATTtgttgt                               <  1:277149/148‑1 (MQ=255)

                                                                                                                 aGCATTATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAGGTTTATGAAGATTTGTTGtta                             <  1:154356/148‑1 (MQ=255)

                                                                                                                 aGCATTATAATTAGTCGCGAAAAAAAAAAGGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAGGTTTATGAAGATTTGTTGtta                             <  1:175052/148‑1 (MQ=255)

                                                                                                                      tATGATTAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAGGTTTATGAAGATTTGTTGTTATTaag                        <  1:242749/148‑1 (MQ=255)

                                                                                                                            tAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAGGTTTATGAAGATTTGTTGTTATTAAGAAGttt                  >  1:43151/1‑148 (MQ=255)

                                                                                                                            tAGACGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAGGTTTATGAAGATTTGTTGTTATTAAGAAGttt                  >  1:78545/1‑148 (MQ=255)

                                                                                                                               aCGCGGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAGGTTTATGAAGATTTGTTGTTATTAAGAAGTTTAAg               <  2:89296/148‑1 (MQ=255)

                                                                                                                                cgcgGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAGGTTTATGAAGATTTGTTGTTATTAAGAAGTTTAAGc              >  1:407583/1‑148 (MQ=255)

                                                                                                                                  cgGAACAAAAAATGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGGTTATTTGAAATTTGATGTAACAGTTGAGGTTTATGAAGATTTGTTGTTATTAAGAAGTTTAAGCGa            >  2:105852/1‑148 (MQ=255)

                                                                                                                                            aaTGGGGAGGGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAGGTTTATGAAGATTTGTTGTTATTAAGAAGTTTAAGCGATTTAAATGaa  >  1:228989/1‑148 (MQ=255)

TGCTGCTTAGATTTCTTATTCATTTTAAAATTCCTCCAATAATTTTTAAGGAGTCAATCAATATCATATAGGTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGGA‑GGGGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAGGTTTATGAAGATTTGTTGTTATTAAGAAGTTTAAGCGATTTAAATGAA  >  CP000730/51180‑51466

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