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	42,835	T→C	28.2%	Q377Q (CAA→CAG)	USA300TCH1516_00035 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	42,835	0	T	C	28.2%	49.2 / 23.5	39	Q377Q (CAA→CAG)	USA300TCH1516_00035	hypothetical protein
Reads supporting (aligned to +/- strand): ref base T (12/16); new base C (3/8); total (15/24)
Fisher's exact test for biased strand distribution p-value = 4.77e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.43e-01

GTTCCACATCAATTTTTCTTTGACTGTAGATATTTTTTGTTTCTGGTTCTGAAAGCTTTTTGTTAATTTGGGATTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCATACTTATCATGACGATAGGCATATCTTTTAAAACCTAGCCGTTTATTATTCGGACAAATGAATTCGTCATT  >  USA300TCH1516_ALE/42696‑42972

gTTCCACATCAATTTTTCTTTGACTGTAGATATTTTTTGTTTCTGGTTCTGAAAGCTTTTTGTTAATTTGGGATTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACAtt                                                                                                                                          >  1:360956/1‑141 (MQ=255)

   ccACATCAATTTTTCTTTGACTGTAGATATTTTTTGTTTCTTGTTCTGAAAGCTTTTTGTTAATTTGGGATTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACACTGAt                                                                                                                                       <  1:253017/141‑1 (MQ=255)

                      gttGTAGATATTTTTTTGTTCTGGTTCTGAAAGCTTTTTGTTAATTTGGGATTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATATACTGACTTTTCAGAGGACATTCTGa                                                                                                                    <  2:331035/139‑1 (MQ=255)

                        tGTAGATATTTTTTGTTTCTGGTTCTGAAAGCTTTTTGTTAATTTGGGATTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCAGAGGACATTCTGAAc                                                                                                                  <  2:169046/141‑1 (MQ=255)

                           aGATATTTTTTGTTTCTGGTTCTGAAAGCTTTTTGTTAATTTGGGATTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCAGAGGACTTTCTGAACAat                                                                                                               >  1:126901/1‑141 (MQ=255)

                            gATATTTTTTGTTTCTGGTTCTGAAAGCTTTTTGTTAATTTGGGATTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCAGAGGACATTCTGAACAatc                                                                                                              <  2:249422/141‑1 (MQ=255)

                              tatTTTTTGTTTCTGGTTCTGAAAGCTTTTTGTTAATTTGGGATTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCAGAGGACATTCTGAACAatcat                                                                                                            >  2:15316/1‑141 (MQ=255)

                               atTTTTTGTTTCTGGTTTTGAAAGCTTTTTGTTAATTTGGGATTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTTATACACTGATTTTTCAGAGGACATTCTGAACAatcatc                                                                                                           <  2:362005/141‑1 (MQ=255)

                                  ttttGTTTCTGGTTCTGAAAGCTTTTTGTTAATTTGGGATTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCAGAGGACATTCTGAACAATCATcaca                                                                                                        >  1:147672/1‑141 (MQ=255)

                                   tttGTTTCTGGTTCTGAAAGCTTTTTGTTAATTTGGGATTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCAGAGGACATTCTGAACAATCATCACAt                                                                                                       <  2:343721/141‑1 (MQ=255)

                                      gTTTCTGGTTCTGAAAGCTTTTTGTTAATTTGGGATTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCa                                                                                                    >  2:262236/1‑141 (MQ=255)

                                               tCTGAAAGCTTTTTGTTAATTTGGGATTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTg                                                                                           >  1:343137/1‑141 (MQ=255)

                                                      gCTTTTTGTTAATTTGGGATTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCACAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGtctc                                                                                    <  2:211471/141‑1 (MQ=255)

                                                        tttttCTTAATTTGGGATTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGc                                                                                  <  1:295823/141‑1 (MQ=255)

                                                            tGTTAATTTGGGATTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTtat                                                                              >  1:130505/1‑141 (MQ=255)

                                                                taTTTGGGATTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAAcc                                                                          <  2:321912/140‑1 (MQ=255)

                                                                aaTTTGGGATTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAAcc                                                                          <  2:322077/141‑1 (MQ=255)

                                                                 aTTTGGGATTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCa                                                                         >  1:126065/1‑141 (MQ=255)

                                                                 aTTTGGGATTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCa                                                                         >  1:49742/1‑141 (MQ=255)

                                                                 aTTTGGGATTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCa                                                                         >  1:301039/1‑141 (MQ=255)

                                                                    tGGGACTTAAAATATTCCCAGTTATAATTCTCCATTAGTTTTTTGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCATAGGACATTCTGAACAATCATCACATTCAAATAATTTCACAGCTCGCTTATAACCATAc                                                                      <  2:182853/141‑1 (MQ=255)

                                                                       taTTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACACTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCATACTTa                                                                   <  1:288773/140‑1 (MQ=255)

                                                                          tttaaaTATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATATATTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCATACTTATCa                                                                <  2:154549/138‑1 (MQ=255)

                                                                                           ataATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACACTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCATACTTATCATGACGATAGGCATATCt                                               <  1:382442/141‑1 (MQ=255)

                                                                                              aTTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCATCCTTATCATGACGATAGGCATATCtttt                                            >  1:149805/1‑141 (MQ=255)

                                                                                              aTTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCATACTTATCATGACGATAGGCATATCtttt                                            >  1:29604/1‑141 (MQ=255)

                                                                                                tcttcATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATCCTTTGATCTTGCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCATACTTATCATGACGATAGGCATATCTTTTaa                                          <  1:225609/141‑1 (MQ=255)

                                                                                                tcttcATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACTTTGATTATTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCATACTTATCATGACGATAGGCATATCTTTTaa                                          <  1:225613/141‑1 (MQ=255)

                                                                                                 cttcATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACACTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTTTCGCTTATAACCATACTTATCATGACGATAGGCATATCTTTTaaa                                         <  1:17333/141‑1 (MQ=255)

                                                                                                       tattTTTTTGTTTGTTTTTTTTTTTTTTTTCATACACTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCATACTTATCTTTACGATAGGCATATCTTTTAAAACCTat                                   >  2:393881/1‑140 (MQ=255)

                                                                                                          ttttttGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCATACTTATCATGACGATAGGCATATCTTTTAAAACCTAGCCg                                <  2:345938/141‑1 (MQ=255)

                                                                                                            ttttGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCATACTTATCATGACGATAGGCATATCTTTTAAAACCTAGCCGtt                              >  1:233361/1‑141 (MQ=255)

                                                                                                              ttgtttgtTTTTGAATTGAAGTTCATACATTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCATACTTATCATGACGATAGGCATATCTTTTAAAACCTAGCCGTtta                            <  2:19377/141‑1 (MQ=255)

                                                                                                               tgtttgttTTTGAATTGAAGTTCATACACTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCATACTTATCATGACGATAGGCATATCTTTTAAAACCTAGCCGTttat                           <  1:337698/141‑1 (MQ=255)

                                                                                                               tgtttgttTTTGAATTGAAGTTCATACACTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCATACTTATCATGACGATAGGCATATCTTTTAAAACCTAGCCGTttat                           <  1:334704/141‑1 (MQ=255)

                                                                                                                                    tCATACACTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCATACTTATCATGACGATAGGCATATCTTTTAAAACCTAGCCGTTTATTGTTCAGACAAATAAATTCgc      >  1:50752/1‑140 (MQ=255)

                                                                                                                                     cATACATTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCATACTTATCATGACGATAGGCATATCTTTTAAAACCTAGCCGTTTATTGTTCGGACAAATGAATTCGTc     <  1:240748/141‑1 (MQ=255)

                                                                                                                                     cATACATTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCATACTTATCATGACGATAGGCATATCTTTTAAAACCTAGCCGTTTATTATTCGGACAAATGAATTCGTc     <  2:50655/141‑1 (MQ=255)

                                                                                                                                       tACATTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCCTATAATTTGCAGTCTCGCTTATATCCATACTTAGCATGACGATAGGCATATCTTTTAAAACCTAGCCGTTTATTATTCGGACAAATGAATTCGTCAt   <  1:15316/141‑1 (MQ=255)

                                                                                                                                       tACACTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCATACTTATAATGTTAATTCGTAAATCATTTAAAACCTAGCCGTTTATTATTCGGACAAATGAATTCGTCAt   >  1:269687/1‑141 (MQ=255)

                                                                                                                                        acacTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCATACTTCTCATGACGATAGGCATATCTTTTAAAACCTAGCCGTTTATTATTCGGACAAATGAATTCGTCAtt  <  2:353836/141‑1 (MQ=255)

GTTCCACATCAATTTTTCTTTGACTGTAGATATTTTTTGTTTCTGGTTCTGAAAGCTTTTTGTTAATTTGGGATTTAAAATATTCCCAGTTATAATTCTTCATTATTTTTTTGTTTGTTTTTGAATTGAAGTTCATACATTGATTTTTCAGAGGACATTCTGAACAATCATCACATTCATATAATTTGAAGTCTCGCTTATAACCATACTTATCATGACGATAGGCATATCTTTTAAAACCTAGCCGTTTATTATTCGGACAAATGAATTCGTCATT  >  USA300TCH1516_ALE/42696‑42972

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A