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 F71 I1 R1	31	24.1	564604	94.3%	532421	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,109,450	T→C	T179A (ACA→GCA)	USA300HOU_RS10675 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,109,450	0	T	C	93.8%	127.2 / NA	48	T179A (ACA→GCA)	USA300HOU_RS10675	hypothetical protein
Reads supporting (aligned to +/- strand): ref base T (1/2); new base C (19/26); total (20/28)
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

AACGTTCTTCTATTTTTCTTTTTACCTAATCCACCACGTTTGACGTTTACCATTTCAGGACCAAAGAAATAATGAATTTCATCAAAAATAACACACCCCTCACGTCCACCGTCTTTGGTTTTTGTGTTTGATGTGTTATATCGAATAACCGATTTAGTTGCACGGTTTATTATTTTTGCTTTACTAACTTCATAAGGAGCTTTTGGCGTTTTACCCGTCTTATTTCGTTTGTTATCCATTAAAACGGTTCTGATTTCATCAAACGA  >  USA300TCH1516_ALE/2109317‑2109582

aaCGTTCTTCTATTTTTCTTTTTACCTAATCCACCACGTTTGACGTTTACCATTTCAGGACCAAAGAAATAATGAATTTCATCAAAAATAACACACCCCTCACGTCCACCGTCTTTGGTTTTTGTGTTTGATGCGTTatat                                                                                                                               >  1:138430/1‑141 (MQ=255)

  cGTTCTTCTATTTTTCTTTTTACCTAATCCACCACGTTTGACGTTTACCATTTCAGGACCAAAGAAATAATGAATTTCATCAAAAATAACACACCCCTCACGTCCACCGTCTTTGGTTTTTGTGTTTGATGCGTTATATCg                                                                                                                             <  1:262853/141‑1 (MQ=255)

        tctATTTTTCTTTTTACCTAATCCACCACGTTTGACGTTTACCATTTCATGACCAAAGAAATAATGAATTTCATCAAAAATAACACACCCCTCACGTCCACCGTCTTTGGTTTTTGTGTTTGATGCGTTATATCGAATAAc                                                                                                                       >  2:164052/1‑141 (MQ=255)

         ctATTTTTCTTTTTACCTAATCCACCACGTTTGACGTTTACCATTTCAGGACCAAAGAAATAATGAATTTCATCAAAAATAACACACCCCTCACGTCCACCGTCTCTGGTTTTTGTGTTTGATGCGTTATATCGAATAAcc                                                                                                                      >  1:80473/1‑141 (MQ=255)

           aTTTTTCTTTTTACCTAATCCACCACGTTTGACGTTTACCATTTCAGGACCAAAGAAATAATGAATTTCATCAAAAATAACACACCCCTCACGTCCACCGTCTTTGGTTTTTGTGTTTGATGCGTTATATCGAATAACCGa                                                                                                                    >  1:34532/1‑141 (MQ=255)

           aTTTTTCTTTTTACCTAATCCACCACGTTTGACGTTCACCATTTCAGGACCAAACAAACAACGCATTTCAGCAAAAATCACACCCCCCTCACGTTCACCTCCTTTCGCTTTTGCGTTTCATCCTTTATCTCGCATTACCgc                                                                                                                    >  2:101973/1‑140 (MQ=255)

            tttttCTTTTTACCTAATCCACCACGTTTGACGTTTACCATTTCAGGACCAAAGAAATAATGAATTTCATCAAAAATAACACACCCCTCACGTCCACCGTCTTTGGTTTTTGTGTTTGATGCGTTATATCGAATAACCgct                                                                                                                   >  2:161506/1‑139 (MQ=255)

                     ttACCTAATCCACCACGTTTGACGTTTACCATTTCAGGACCAAAGAAATAATGAATTTCATCAAAAATAACACACCCCTCACGTCCACCGTCTTTGGTTTTTGTGTTTGAAGCGCTATATCGAATCACCGATTTAGTTTCa                                                                                                          >  1:190985/1‑141 (MQ=255)

                         cTAATCCACCACGTTTGACGTTTACCATTTCAGGACCAAAGAAATAATGAATTTCATCAAAAATAACACACCCCTCACGTCCACCGTCTTTGGTTTTTGTGTTTGATGCGTTATATCGAATAACCGATTTAGTTGCACGGt                                                                                                      >  1:222750/1‑141 (MQ=255)

                          tAATCCACCACGTTTGACGTTTACCATTTCAGGACCAAAGAAATAATGAATTTCATCAAAAATAACACACCCCTCACGTCCACCGTCTTTGGTTTTTGTGTTTGATGCGTTATATCGAATAACCGATTTAGTTGCACGGtt                                                                                                     <  1:70285/141‑1 (MQ=255)

                           aaTCCACTACGTTTGACGTTTACCACCACCGCGCTATAGTAATAATGAATTTCATCAACAATAACACACCCCTCACGTCCACCGTCTTTGGTTTTTGTGTTTGATGCGTTATATCGAATAACCGATTTAGTTGCACGGttt                                                                                                    <  2:257592/141‑1 (MQ=255)

                           aaTCCACCACGTTTGACGTTTACCATTTCAGGACCAAAGAAATAATGAATTTCATCAAAAATAACACACCCCTCACGTCCACCGTCTTTGGTTTTTGTGTTTGATGCGTTATATCGAATAACCGATTTAGTTGCACGGttt                                                                                                    >  1:221133/1‑141 (MQ=255)

                             tCCACCACTTTTGACGTTTACCATTTCAGGACCAAAGAAATAATGAATTTCATCAAAAATAACACACCCCTCACGTCCACCGTCTTTGGTTTTTGTGTTTGATGCGTTATATCGAATAACCGATTTAGTTGCACGGTttat                                                                                                  <  1:75510/141‑1 (MQ=255)

                             tCCACCACGTTTGACGTTTACCATTTCAGGACCAAAGAAATAATGAATTTCATCAAAAATAACACACCCCTCACGTCCACCGTCTTTGGTTTTTGTGTTTGATGCGTTATATCGAATAACCGATTTAGTTGCACGGTttat                                                                                                  <  2:43108/141‑1 (MQ=255)

                                   acGTTTGACGTTTACCATTTCAGGACCAAAGAAATAATGAATTTCATCAAAAATAACACACCCCTCACGTCCACCGTCTTTGGTTTTTGTGTTTGATGCGTTATATCGGATAACCGATTTAGGTGCACGGGTTATTCtttg                                                                                            >  1:87237/1‑140 (MQ=255)

                                     gTTTGACGTTTACCATTTCAGGACCAAAGAAATAATGAATTTCATCAAAAATAACACACCCCTCACGTCCACCGTCTTTGGTTTTTGTGTTTTATTTGTTATATCGAATAACCCATTTAGTTGCACGTTTTTTTAtttttt                                                                                          >  2:75150/1‑140 (MQ=255)

                                      tttGACGTTTACCATTTCAGGACCAAAGAAATAATGAATTTCATCAAAAATAACACACCCCTCACGTCCACCGTCTTTGGTTTTTGTGTTTGATGCGTTATATCGAATAACCGATTTAGTTGCACGGTTTATTATTTTTGc                                                                                         <  2:17153/141‑1 (MQ=255)

                                       ttGACGTTTACCATTTCAGGACCAAAGAAATAATGAATTTCATCAAAAATAACACACCCCTCACGTCCACCGTCTTTGGTTTTTGTGTTTGATGCGTTATATCGAATAACCGATTTAGTTGCAAGGTTTATTACTTTTGCt                                                                                        >  2:265447/1‑141 (MQ=255)

                                         tacttttACCATTTCAGGACTATAGAAATCATAAATTTCATCAAAAATAACACACCCCTCACGTCCACCTTCTTTGGTTTTTGTGTTTGATGCGTTATAGCGAATAACCGATTTAGCTGCACGGTTTATTATTTTTGCttt                                                                                      <  2:246495/137‑1 (MQ=255)

                                         gACGTTTACCATTTCAGGACCAAAGAAATAATGAATTTCATCAAAAATAACACACCCCTCACGTCCACCGTCTTTGGTTTTTGTGTTTGATGCGTTATATCGAATAACCGATTTAGTTGCACGGTTTATTATTTTTGCttt                                                                                      >  1:209174/1‑141 (MQ=255)

                                         gACGTTTACCATTTCAGGACCAAAGAAATAATGAATTTCATCAAAAATAACACACCCCTCACGTCCACCGTCTTTGGTTTTTGTGTTTGATGCGTTATATCGAATAACCGATTTAGTTGCACGGTTTATTATTTTTGCttt                                                                                      <  1:161173/141‑1 (MQ=255)

                                                  cATTTCAGGACCAAAGAAATAATGAATTTCATCAAAAATCACACACCCCTCACGTCCACCGTCTTTGGTTTTTGTGTTTGATGCGTTATATCGAATAACCGATTTAGTTGCACGGTTTATTATTTTTGCTTTACTAACTTc                                                                             <  1:27053/141‑1 (MQ=255)

                                                        aGGACCAAAGAAATAATGAATTTCATCAAAAATAACACACCCCTCACGTCCACCGTCTTTGGTTATTGTGTTTGATACGTTATATCGAATAACCGATTTAGTTGCACGGTTTATTATTTTTGCTTTACTAACTTCATatat                                                                       >  2:170592/1‑138 (MQ=255)

                                                         ggACCACAGAAATAATGAATTTCATCAAAAATAACACACCCCCCACGTCCACCTTCTTTGGTTTTTGTGTTTGATGCGTTATATCGAATAACCGATTTAGTTGCACGGTTTATTATTTTTGCTTTACTAACTTCATAAGGa                                                                      <  1:168523/141‑1 (MQ=255)

                                                         ggACCAAAGAAATAATGAATTTCATCAAAAATAACGCACCCCTCACGTCCACCGTCTTTGGTTTTTGTGTTTGATGCGTTATATCGAATAACCGATTTAGTTGCACGGTTTATTATTTTTGCTTTACTAACTTCATAAGGa                                                                      <  2:206039/141‑1 (MQ=255)

                                                          gACCAAAGAAATAATGAATTTCATCAAAAATAACACACCCCTCACGTCCACCGTCTTTGGTTTTTGTGTTTGATGCGTTATATCGAATAACCGATTTAGTTGCACGGTTTATTATTTTTGCTTTACTAACTTTATAAGGAg                                                                     >  2:253518/1‑141 (MQ=255)

                                                          gACCAAAGAAATAATGAATTTCATCAAAAATAACACACCCCTCACGTCCACCGTCTTTGGTTTTTGTGTTTAATGCGTTATATCGAATAACCTATTTAGTTTCACGGTTTATTATTTATACAATACTAACTTTAAAAGGaa                                                                     >  2:226101/1‑140 (MQ=255)

                                                               aaGCAATAATGAATTTGATCAAAAATAACACACACTTGACGTCCACCGTCTTTGGTTTTTGTGTTTGATGCGTTATATCGAATAACCGATTTAGTTGCTCGGTTTATTATTTTTGCTTTACTAACTTCATAAGGAGCtttt                                                                <  2:80473/141‑1 (MQ=255)

                                                                    ataatGAATTTCATCAAAAATAACACACCCCTCACGTCCACCGTATTTGGTTTTTGTGTTTGATGCGTTATATCGAATACCTGATTTCGTTGCACGGTTTATTCTTTTTGCTTTACTATATTCATAAGAAGCTTCTgctgt                                                           >  2:238923/1‑137 (MQ=255)

                                                                     taatGAATTTCATCAAAAATAACACACCCCTCACGTCCACCGTCTTTGGTTTTTGTGTTTGATGCGTTATATCGAATAACCGATTTAGTTGCACGGTTTATTATTTTTGCTTTACTAACTTCATAAGGAGCTTTTGGCGtt                                                          <  2:180410/141‑1 (MQ=255)

                                                                       atGAATTTCATCACAAATAACACACCCCTCACGTCCACCGTCTTTGGTTTTTGTGTTTGATGCGTTATATCGAATAACCGATTTAGTTGCACGGTTTATTATTTTTGCTTTACTAACTTCATAAGGAGCTTTTGGCGtttt                                                        <  1:46796/141‑1 (MQ=255)

                                                                       atGAATTTCATCAAAAATAACACACCCCTCACGTCCACCGTCTTTGGTTTTTGTGTTTGATGCGTTATATCGAATAACCGATTTAGTTGCACGGTTTATTATTTTTGCTTTACTAACTTCATAAGGAGCTTTTGGCGtttt                                                        <  1:171477/141‑1 (MQ=255)

                                                                                atcaAAAATAACACACCCCTCACGTCCACCGTCTTTGGTTTTTGTGTTTTATGCGTTATATCGAATAACCGATTTAGTTGCACGGTTTATTTATTTAACGTTACTAACTTCATAAGGAGCTTTTGGCGTTTTACCCGTCtt                                               >  2:273048/1‑141 (MQ=255)

                                                                                                  cTCACTCCCACCGTCTTTCGTTTTTGTGTGTGATGCGTTATATCGAATAACCGATTTAGTTGCACGGTCTATTATTTTTGGTGTACTAACTTCATAAGGAGCTTTTGGCGTTTTACCCGTCTTATTTCGTTTGTTATCCAt                             <  1:19767/141‑1 (MQ=255)

                                                                                                  cTCACGTCCACCGTCTTTGGTTTTTGTGTTTGATGCGTTATATCGAATAACCGATTTAGTTGCACGGTTTATTATTTTTGCTTTACTAACTTCATAAGGAGCTTTTGGCGTTTTACCCGTCTTATTTCGTTTGTTATCCAt                             >  2:192836/1‑141 (MQ=255)

                                                                                                      cGTCCACCGTCTTTGGTTTTTGTGTTTGATGCGTTATATCGAATAACCGATTTAGTTGCACGGTTTATTATTATTGCTTGTGTAACGTCCTAAGTCGCTCTTGGCGTTTTACCCGTCTTATTTCGTTTGTTATCCATTaaa                         <  1:164052/141‑1 (MQ=255)

                                                                                                       ggccACCGTCTTTGGTTTTTGTGTTTGATGCGTTATATTGGATAACCGATTGAGTTGCACGGTTTATTATTTTTGCTTTACTAACTTCATAGGGAGCTTTTGGCGTTTTACCCGTCTTATTTCGTTTGTTATCCATTaaaa                        <  2:63868/139‑1 (MQ=255)

                                                                                                       gTCTACCGTCTGTGGTTTTTGTGTATGATCTGTTATATCGAATAACCGATTTAGTTGCACGGTTTATTATTTTTGCTTTACTAACTTCATAAGGAGCTTTTGGCGTTTTACCCGTCTTATTTCGTTTGTTATCCATTaaaa                        <  2:257191/141‑1 (MQ=255)

                                                                                                       gTCCACCGGCTGTGGTTTTTGTGTTTGATGCGTTATCTTGGATAACCGATTTTGGTGCTCGGTTTATTATTTTTGCTTTACTAACTTCATAAGGAGCTTTTGGCGTTTTACCCGTCTTATTTCGTTTGTTATCCATTaaaa                        <  2:114144/141‑1 (MQ=255)

                                                                                                        tCCACCGTCTTTGGTTTTTGTGTTTGATGCGTTATATCGAATAACCGATTTAGTTGCACGGTTTATTATTTTTGCTTTACTAACTTCATAAGGAGCTTTTGGCGTTTTACCCGTCTTATTTCGTTTGTTATCCATTAAAAc                       <  1:215339/141‑1 (MQ=255)

                                                                                                          cACCGTCTTTGGTTTTTGTGTTTGATGCGTTATATCGAATAACCGATTTAGTTGCACGGTTTATTATTTTTGCTTTACTAACTTCATAAGGAGCTTTTGGCGTTTTACCCGTCTTATTTCGTTTGTTATCCATTAAAACgg                     <  1:13434/141‑1 (MQ=255)

                                                                                                          cACCGTCTTTGGTTTTTGTGTTTGATGCGTTATACCGAATAACCGATTTAGTCGCACGGTTTATTATCTTTGCTTTACTAACTTCATAAGGAGCTTTTGGCGTTTTACCCGTCTTATTTCGTTTGTTATCCATTAAAACgg                     <  1:13184/141‑1 (MQ=255)

                                                                                                                  ttGGTTTTTGTGTTTGATGCGTTATATCGAATAACCGATTTAGTTGCACGGTTTATTATTTTTGCTTTACTAACTTCATAAGGAGCTTTTGGCGTTTTACCCGTCTTATTTCGTTTGTTATCCATTAAAACTGTTCTGAtt             >  2:55428/1‑141 (MQ=255)

                                                                                                                      tttttGTGTTTGATGCGTTATATCGAATAACCGATTTAGTTGCACGGTTTATTATTTCTGCTTTACTAACTTCATAAGGTGCTTTTGGCTTTTTACCCGTCTTATTTCGTTTGTTATCCATTAAAACGGTTCTGATTtcat         <  1:128739/141‑1 (MQ=255)

                                                                                                                             ttttGATGCGTTATATCGAATAACCGATTTAGTTGCACGGTTTATTATTTTTGCTTTACTAACTTCATAAGGAGCTTTTGGCGTTTTACCCGTCTTATTTCGTTTGTTATCCATTAAAACGGTTCTGATTTCATCAAACGa  <  2:161401/140‑1 (MQ=255)

                                                                                                                             gtTTGATGCGTTATATCGAATAACCGATTTAGTTGCACGGTTTATTATTTTTGCTTTACTAACTTCATAAGGAGCTTTTGGCGTTTTACCCGTCTTATTTCGTTTGTTATCCATTAAAACGGTTCTGATTTCATCAAACGa  <  2:19028/141‑1 (MQ=255)

                                                                                                                             gtTTGATGCGTTATATCGAATAACCGATTTAGTTGCACGGTTTATTATTTTTGCTTTACTAACTTCATAAGGAGCTTTTGGCGTTTTACCCGTCTTATTTCGTTTGTTATCCATTAAAACGGTTCTGATTTCATCAAACGa  <  1:146320/141‑1 (MQ=255)

                                                                                                                             ggttGATGTGGTAGATGGAAGAACCGATTGAGTTGCACGGTGTATTATGTTTGCTTTAGTAACTTCATAAGGAGCTTTTGGCGTTTTACCCGTCTTATGTGGTTTGTTATCCATGAAAACGGTTCTGATTTCATCAAACGa  <  2:20095/139‑1 (MQ=255)

AACGTTCTTCTATTTTTCTTTTTACCTAATCCACCACGTTTGACGTTTACCATTTCAGGACCAAAGAAATAATGAATTTCATCAAAAATAACACACCCCTCACGTCCACCGTCTTTGGTTTTTGTGTTTGATGTGTTATATCGAATAACCGATTTAGTTGCACGGTTTATTATTTTTGCTTTACTAACTTCATAAGGAGCTTTTGGCGTTTTACCCGTCTTATTTCGTTTGTTATCCATTAAAACGGTTCTGATTTCATCAAACGA  >  USA300TCH1516_ALE/2109317‑2109582

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A