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 F178 I0 R1	41	49.4	1100758	95.6%	1052324	140.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,289,257	A→C	66.6%	V78G (GTA→GGA)	cdaA ←	Cyclic di‑AMP synthase CdaA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,289,257	0	A	C	66.6%	44.0 / 16.5	41	V78G (GTA→GGA)	cdaA	Cyclic di‑AMP synthase CdaA
Reads supporting (aligned to +/- strand): ref base A (7/7); new base C (13/14); total (20/21)
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

TTTGAAACCGATTGAATCAATTTCTCTTCATCTTTACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTAAAGACCGTG  >  USA300TCH1516_ALE/2289122‑2289391

tttGAAACCGATTGAATCAATTTCTCTTCATCTTTACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATCcccc                                                                                                                                    >  2:446651/1‑140 (MQ=255)

   gAAACCGATTGAATCAATTTCTCTTCATCTTTACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATCCCCCCCa                                                                                                                                 <  1:462687/140‑1 (MQ=255)

    aaaCCGATTGAATCAATTTCTCTTCATCTTTACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATCCCCCCCAt                                                                                                                                <  1:172162/140‑1 (MQ=255)

              aaTCAATTTCTCTTCATCTTGACTATACGTATTAGAAGTATAGCATTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTATAATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCCCATTGAATAACGa                                                                                                                      >  2:301666/1‑140 (MQ=255)

                       ctctTCATCTTTACTATACGTATTAGAAGTATAGCGTTTTAAAATTCTTAGTACACCAAATTGTTTTTAATCACATCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATCCCCCCAATTGAATAACGTAATCGaata                                                                                                             >  1:264526/1‑140 (MQ=255)

                         ctTCATCTTTACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCCCATTGAATAACGATATGGaataat                                                                                                           >  2:502797/1‑140 (MQ=255)

                                   aCTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATCCCCCCCATTGAATACCGATAACAACTAATTTCGATGTTg                                                                                                 >  2:163636/1‑140 (MQ=255)

                                   aCTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACACACGACTAATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTg                                                                                                 >  1:3236/1‑140 (MQ=255)

                                     tataCGTATTAGAATTATAGCGTTTTAAAAAGCTACCGCTACCAAGTTGTTCTAACGTACGTCTAATTTCTGGTTGGAATATTACTATTAACGCTAATACCCCCCATTGAATAACGATTTCGAATAATTTAGATGTTGCa                                                                                               <  2:365314/140‑1 (MQ=255)

                                       taCGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGt                                                                                             <  2:50742/140‑1 (MQ=255)

                                       taCGAATGAGAAGTATAGACTTTTAAAAAGCTACCTCCACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATACACCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGt                                                                                             <  2:492329/140‑1 (MQ=255)

                                           tATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTACAGTCAAg                                                                                         >  1:205920/1‑140 (MQ=255)

                                            aTTAGAAGTATATCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATCCCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGt                                                                                        <  2:81515/140‑1 (MQ=255)

                                            aTTAGAAGTATAGCATTTTAACAAGCTACCTCTACCAAGTTGTTCTAACACACGTCTAATTTCTGGTTGGAATATAACTATTAAAGATAAAACCCCCCATTGAATAACGATATCGAATAATTTAAACGTTGCAGTCAAGt                                                                                        >  1:287377/1‑140 (MQ=255)

                                                  aGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATCCCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCACATTCAata                                                                                  >  2:385152/1‑140 (MQ=255)

                                                  aGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATCCCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAata                                                                                  >  1:284893/1‑140 (MQ=255)

                                                  aGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATCCCCCCCATTGAATAACGATATCGAATAAATTAAATGTGGCAGTCAAGTTCAata                                                                                  >  2:27509/1‑140 (MQ=255)

                                                      taGCTTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATCCCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCAt                                                                              <  2:539299/140‑1 (MQ=255)

                                                      taGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATCCCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATAAt                                                                              >  2:71486/1‑140 (MQ=255)

                                                      taGCGTTTTAAAAAGCTACCTCTACCAAGTTATTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAAACCCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCAt                                                                              <  1:263100/140‑1 (MQ=255)

                                                         cGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATCCCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACt                                                                           >  1:79475/1‑140 (MQ=255)

                                                          gTTTTACAAAGCTACCTCTACCAAGTTTTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATCCCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACtt                                                                          <  1:481334/140‑1 (MQ=255)

                                                           ttttAAAAAGTTACCTCTATCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGTAATATTACTATTAAAGCTAATCCCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTa                                                                         <  1:198205/140‑1 (MQ=255)

                                                           ttttAAAAAGCTACCTCTCCCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTCTTAAAGCTAATCCCCCCCATTCAATAACCATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTa                                                                         <  2:203003/140‑1 (MQ=255)

                                                                 aaaGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATCCCCCCCTTTGAATAACGATATCGAATTATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATctgct                                                                   <  1:429986/140‑1 (MQ=255)

                                                                   aGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAGGTCCAATATCCTCATTATctgctgg                                                                 >  2:106291/1‑139 (MQ=255)

                                                                         ctctACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATCCCCCCCATTGCATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATa                                                           >  2:291267/1‑140 (MQ=255)

                                                                           ctACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATCCCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAAc                                                         >  1:531258/1‑140 (MQ=255)

                                                                                               aCGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATCCCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTaa                                     >  1:466801/1‑140 (MQ=255)

                                                                                                 gTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATCCCCCCCATTGAATAACGATATCGAATAATTTATATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGt                                   <  1:528256/140‑1 (MQ=255)

                                                                                                 gTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATCCCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGt                                   <  1:528186/140‑1 (MQ=255)

                                                                                                     tatgtCTGGTTTGAATAATAATTTTAAAGCTAATACCCCCCATTTAATAACGATATCGAATTATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATTTCCCTTTAAGTAAtt                               <  2:247459/136‑1 (MQ=255)

                                                                                                          ctggctggAATATTACTATTAAAGCTAATCCCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATc                          <  2:2488/140‑1 (MQ=255)

                                                                                                           tGGTTGGAATATTACTATTAAAGCTAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTATATCg                         >  1:74853/1‑140 (MQ=255)

                                                                                                                  aaTATTACTATTAGAGCTAATACCCCCCATGGAATAACGATATCGAATAATTTATATGTTGAAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGt                  <  1:114629/140‑1 (MQ=255)

                                                                                                                      ttACTATTAAAGCTAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTccc              <  2:83609/140‑1 (MQ=255)

                                                                                                                           aTTAAAGCTAATACCCCCCATTAAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTaaa         <  2:340825/140‑1 (MQ=255)

                                                                                                                                aGCTAATCCCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTAAAGACCg    <  1:60468/140‑1 (MQ=255)

                                                                                                                                 gCTAATCCCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTAAAGACCGt   >  1:315451/1‑140 (MQ=255)

                                                                                                                                 gCTAATCCCCCCCATTGAATAACGATATCAAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTAAAGACCGt   <  2:233686/140‑1 (MQ=255)

                                                                                                                                  cTAATCCCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCATGTTCAATATCATACTTATCTACTTACCAATAACAATTACTAATATCCATTTAATTAATTGTATCGCTTTAGTTTCCTTAAAGACCGtg  >  1:237328/1‑140 (MQ=255)

TTTGAAACCGATTGAATCAATTTCTCTTCATCTTTACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTAAAGACCGTG  >  USA300TCH1516_ALE/2289122‑2289391

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