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 F70 I1 R1	12	27.5	645536	94.4%	609385	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,279,705	G→A	A943V (GCA→GTA)	ebh_3 ←	Extracellular matrix‑binding protein ebh

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,279,705	0	G	A	96.9%	78.7 / NA	32	A943V (GCA→GTA)	ebh_3	Extracellular matrix‑binding protein ebh
Reads supporting (aligned to +/- strand): ref base G (0/0); major base A (12/19); minor base C (0/1); total (12/20)
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

AGTTGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTGCTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGAATTTGCTGT  >  USA300TCH1516_ALE/2279581‑2279841

acctGATTCGACTTCTGGTTTACTAGTCACATCGTTACCCATTGTCGGACTGTTTGTTGATGCTTCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCGGATGTTACTGTTGTTTCACCTGt                                                                                                                          <  1:140735/138‑1 (MQ=255)

  ttGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTg                                                                                                                        <  1:23633/141‑1 (MQ=255)

    taTTCTTCTTCTGGTTTGCTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACATTAGAATTGTTGTTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTggc                                                                                                                      <  2:139553/140‑3 (MQ=255)

    gATTCTACTTCTGGTTTACTCGTTACATCGTGATCCATTGTCGGACTGGTTGTTGATGCATCTACACTAGAATTGTTCTTCGCTTGCCGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGcc                                                                                                                      <  1:312336/141‑1 (MQ=255)

      ttCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGc                                                                                                                    <  1:281021/141‑1 (MQ=255)

          aCTGCTGGTTTAATAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATACATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATTTTACCGTTTTTTCACCTGTTGCCGCATCa                                                                                                                >  2:134472/1‑141 (MQ=255)

             tCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACta                                                                                                             >  1:212462/1‑141 (MQ=255)

              cTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTTCATCATCAGTTGCTGATGTTACTGTTGTTTCCCCTTTTGCCTCATCTCtat                                                                                                            >  2:7527/1‑141 (MQ=255)

              cTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGTTGATGTTACTGTTGTTTCACATTTTGCCGAATCACtat                                                                                                            >  2:94909/1‑141 (MQ=255)

               tGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACtatt                                                                                                           >  2:206430/1‑141 (MQ=255)

                 gTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGAATCATCAGTTACTGATGTTACTGTTGTTTCACATGTTGACGCATCACtattat                                                                                                         >  1:109145/1‑141 (MQ=255)

                    tACTAGTTATTGTGTTATCCAGTGTCTGGCTGTTTGTTTATGCATCTATACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTTCTGAGGTTCCTGTTGGTTCAACTGTTGCCGCAGCACGATTATTTg                                                                                                      <  2:28634/141‑1 (MQ=255)

                    tACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTATCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTg                                                                                                      <  2:205635/141‑1 (MQ=255)

                                                     ttgttgATGCTTCTTCATTAGACTTCTTACTAGCTTGCGGTTTATCATTTGCCTCATCAGCTGCTCATGTTACTGTCGTTTCACCTGTTGCCGCCTCTCTATTCTTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAg                                                                     <  2:223995/141‑1 (MQ=255)

                                                       gttgATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGTAGCGTCTGCTTTGCCATTAGCt                                                                   >  1:112409/1‑141 (MQ=255)

                                                          gATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTgtc                                                                <  1:25166/141‑1 (MQ=255)

                                                            ttcATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCAGCATCAGTGGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTgtcgt                                                              <  1:118574/139‑1 (MQ=255)

                                                                    cacTGGAATTTTTATTAGGATGCGGTTTATCATTTGTATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATa                                                      <  2:258065/141‑1 (MQ=255)

                                                                      cTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACg                                                    >  1:32880/1‑141 (MQ=255)

                                                                                    aGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGt                                      >  1:170408/1‑141 (MQ=255)

                                                                                       ttGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATCCGTTCGGTTGTCCAGTAtt                                   >  1:112423/1‑141 (MQ=255)

                                                                                              ttATCATTTGCATCATCAGTTGCTGATGGTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGgt                            <  1:155932/141‑1 (MQ=255)

                                                                                                aTCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTTGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGgtgt                          <  2:212462/141‑1 (MQ=255)

                                                                                                    tttGCATGATCAGTTGCTTATGTTACTGTTGTTTCACTTGTTGCCGCATCACTATTGTTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCTTTAGCTGTCGTCTCAGTTACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCa                      <  2:74689/141‑1 (MQ=255)

                                                                                                      tGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCAtt                    >  1:209584/1‑141 (MQ=255)

                                                                                                      tGCATCATCAGTTGCTGATGTTACGGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCAtt                    <  1:40086/141‑1 (MQ=255)

                                                                                                          tcatcaGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTTTATTAGCa                >  2:191609/1‑141 (MQ=255)

                                                                                                             tcaGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCAttt             <  2:202440/141‑1 (MQ=255)

                                                                                                                ggtGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGaa          <  1:213790/139‑1 (MQ=255)

                                                                                                                 ttGCTGATGGTACTGTTGTTTCACCTGTTGCCGCGTCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGAAt         <  2:250034/141‑1 (MQ=255)

                                                                                                                     tGATGTTACTGTTGTTTCCCCTGTTCCCTCATCACGATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGAATTTGc     <  1:302043/141‑1 (MQ=255)

                                                                                                                      gATGTTACTGTTGTTTCGTCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATAAGGTGTTGTCTCAGCTACGTGAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGAATTTGCt    <  2:21523/141‑1 (MQ=255)

                                                                                                                        ttttgttgttgTTTCACTTGTTGCCTCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGAATTTGCTGt  <  2:316568/139‑1 (MQ=255)

AGTTGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTGCTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGAATTTGCTGT  >  USA300TCH1516_ALE/2279581‑2279841

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