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
A17 F172 I0 R1	42	33.2	716278	96.8%	693357	139.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	2,021,817	C→T	100%	V139I (GTT→ATT)	USA300HOU_1873 ←	acyl‑CoA hydrolase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,021,817	0	C	T	96.3%	111.3 / ‑4.8	40	V139I (GTT→ATT)	USA300HOU_1873	acyl‑CoA hydrolase
Reads supporting (aligned to +/- strand): ref base C (1/1); new base T (17/21); total (18/22)
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
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ACAATCTGTCTTTATATTTTTAGTCTCTAATATGTTGCACTTGAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAACATC‑ATCTTC‑TGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGCAACAAATGTTAAGTAACTTAATGCAGCTAAATCATGCTTGTTATTAAATACATCGTCAATTCTAATTTGAACGACCACT  >  CP000730/2021682‑2021953

aCAATCTGTCTTTATATTTTTAGTCTCTAATATGTTGCACTTGAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAAtatc‑a                                                                                                                                       <  1:272247/140‑1 (MQ=255)

 cAATCTGTCTTTATATTTTTAGTCTCTAATATGTTGCACTTGAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAAtatc‑at                                                                                                                                      <  2:246397/140‑1 (MQ=255)

        tCTTTATATTTTTAGTCTCTAATATGTTGCACTTGAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAATATC‑ATCTTC‑Tgg                                                                                                                              <  1:268808/140‑1 (MQ=255)

        tCTTTATATTTTTAGTCTCTAATATGTTGCACTTGAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTAATGGTTCTGTATCATAAAACCATTTTTCAATATC‑AACTTC‑Tgg                                                                                                                              >  1:9152/1‑140 (MQ=255)

         cTTTATATTTTTAGTCTCTAATATGTTGCACTTGAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTCGTGGTGCTGTATCATAAAACCATTTTTCAATATC‑ATCTTC‑TGGa                                                                                                                             >  1:203029/1‑140 (MQ=255)

         cTTTATATTTTTAGTCCCTAATATGTTGCACTTGAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAATATC‑ATCTTC‑TGGa                                                                                                                             <  2:217292/140‑1 (MQ=255)

          tttATATTTTTAGTCTCTAATATGTTGCACTTGAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAATATC‑ATCTTC‑TGGat                                                                                                                            >  2:310212/1‑140 (MQ=255)

          tttATATTTTTAGTCTCTAATATGTTGCACTTGAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAATATC‑ATCTTC‑TGGat                                                                                                                            >  2:310112/1‑140 (MQ=255)

             atatTTTTAGTCTCTAATATGTTGCACTTGAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAATATC‑ATCTTC‑TGGAtata                                                                                                                         <  1:138596/140‑1 (MQ=255)

                      ggctctAATAGGTTGCACCTGAGCGAAATATTCAATTGTTTGTTTTCTTGCACTTCCACATTCTTTTCTTCGTCTAACACGTTGTGGGTCTGTATCATAAAACCATTTTGCAATATC‑ATCTTC‑TGGATATACACCAGTTa                                                                                                                <  2:83602/138‑1 (MQ=255)

                      gTCTCTAATATGTTGCACTTGAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAATATC‑AGCTTC‑TGGATATACACCTGGTa                                                                                                                >  2:272593/1‑140 (MQ=255)

                            aaTATGTTGCACTTGAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAATATC‑ATCTTC‑TGGATATACACCAGGTACATGtt                                                                                                          >  1:337021/1‑140 (MQ=255)

                               atGTTGCACTTGAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAATATC‑ATCTTC‑TGGAAATACACCAGGTACATgataag                                                                                                       >  1:115871/1‑135 (MQ=255)

                                tGTTGCACTTTAGCTAAATATTCAATTGTTTGATTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAATATC‑ATCTTC‑TGGATATACACCAGGTACATGTTTAgg                                                                                                      <  1:93947/140‑1 (MQ=255)

                                   ctcACGTGATCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAATATC‑ACCTTC‑TGGATATACACCAGGTACATGTTTAGGttt                                                                                                   <  2:35848/138‑1 (MQ=255)

                                         tGAGCTAAATATTCAATTGTTAGCTCCCATTCAATGCGACGTGCTTTTCTTAGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAATATC‑ATCTTC‑TGGATATACACCAGGTACATGTTTAGGTTTGCCTtc                                                                                             >  2:252940/1‑140 (MQ=255)

                                              tAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAATATC‑ATCTTC‑TGGATATACACCAGGTACATGTTTAGGTTTGCCTTcatcat                                                                                        <  1:344777/140‑1 (MQ=255)

                                                   atTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAATATC‑ATCTTC‑TGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAAc                                                                                   <  1:310212/140‑1 (MQ=255)

                                                   atTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAATATC‑ATCTTC‑TGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAAc                                                                                   <  1:310112/140‑1 (MQ=255)

                                                    ttCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAATATC‑ATCTTC‑TGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACg                                                                                  <  1:338160/140‑1 (MQ=255)

                                                      cAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAATATC‑ATCTTC‑TGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGca                                                                                >  2:35205/1‑140 (MQ=255)

                                                        aTTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAATATC‑ATCTTC‑TGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGcaac                                                                              <  1:226616/140‑1 (MQ=255)

                                                        aTTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTT‑‑GCGTCGGTCTCCTTGGATCTAAATCAGGTTCATGTTTAGTTTTACCTTCATCATCTAGCgtgac                                                                              >  1:82316/1‑136 (MQ=255)

                                                         ttgtttgtTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAATATC‑ATCTTC‑TGGATATACACCAGGTACATATTTAGGTTTGCCTTCATCATCTAACGcaaca                                                                             >  1:285511/1‑140 (MQ=255)

                                                                tttACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTAGTGGTGCTGTATCATAAAACCATTTTTCAATATA‑ATCTTC‑TGGATATACACAAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGCAACCAATGTTa                                                                      >  2:157577/1‑140 (MQ=255)

                                                                    cTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAATATC‑ATCTTC‑TGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGCCACAACTGTTAAGtc                                                                  >  1:22411/1‑139 (MQ=255)

                                                                      ttaaaTGCGACGTGCTTTTCTTCGTTAAACACGGTGTGGTGCTGTTTGATAGAACCGTGTGTAAATATC‑GTCTTC‑TGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGCAACAAATGTTAAGTAAc                                                                <  1:154547/137‑1 (MQ=255)

                                                                      ttCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAATTTC‑ATCTTC‑TGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTATCGCAACAAATGTTGAGTAAc                                                                >  1:79160/1‑140 (MQ=255)

                                                                               aCGTGCTTTTCTTCGTTCAACACGTTTTGGTGCTGTATCATAAAACCATTTTTCAATATC‑ATCTTC‑TGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGCAACAAATGTTAAGTAACTTAATGCAg                                                       <  1:312136/140‑1 (MQ=255)

                                                                                   gCTTTTCTTCGTTCAACACGTTGTGGTGCCGTATCAGAAAACCAGTTTGCAATATC‑ATCTTC‑TGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGCAACAAATGTTAAGTAACTTAATGCAGCTaa                                                   <  2:187832/140‑1 (MQ=255)

                                                                                      tttCTTCGTTCAACACGTTGTGGGGCTGTATCATAAAACCATTTTTCAATATC‑ATCTTC‑TGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGCAACAAATGTTAAGTAACTTAATGCAGCTAAATc                                                <  2:203029/140‑1 (MQ=255)

                                                                                          ctcGTTTCACACGTTGTGGTGCTGGAGCATAAAGCCATGTTTCCATATC‑ATCTTC‑TGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGCAACAAATGTTAAGTAACTTAATGCAGCTAAATCATGc                                            <  2:320790/139‑1 (MQ=255)

                                                                                            cGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAATATC‑ATCTTC‑TGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGCAACAAATGTTAAGTAACTTAATGCAGCTAAATCATGCtt                                          <  1:35205/140‑1 (MQ=255)

                                                                                                cAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAATATG‑ATCTTC‑TGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGCACCAAATGTTAAGTAACTTAATGCAGCTAAATCATGCTTGtta                                      >  1:231812/1‑140 (MQ=255)

                                                                                                   cacGTTGTGTGGCCGCATCAGAAAACCATTTGTCCACATC‑ATCTTC‑TGAATATACACCAGGCACATGTTTACGTTCTCCTTCCTCATCTAACGCAACAAATGTCTACTAACTTGTCGCAATTCAATCATGCGTGttaccc                                   <  2:4981/140‑4 (MQ=255)

                                                                                                   cacGTTGTGGTGCTGTATCATAAAACCATTTTTCAATATC‑ATCTTC‑TGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGCAACAAATGTTAAGAAACTAAATGCATCTAAATCATGATTGttatta                                   >  1:1269/1‑140 (MQ=255)

                                                                                                     cGTTCTGGTTCTGTATCATAAAACCATTTTTCAATATC‑ATCTTC‑TGGATATACACCAGGTACATGTTTAGGTTTGCCTTTATCATCTAACGCAACAAATGTTAAGTAACTTAATGCAGCTAAATCATGCTTGTTATTaaa                                 <  1:21773/140‑1 (MQ=255)

                                                                                                         gtggtgCTGTATCATAAAACCATTTTTCAATATC‑ATCCTC‑TGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCAACTAACGCAACAAATGTTAAGTAACTTAACGCAGCTAAATCATGCTTGTTATTAAATACa                             <  2:22139/140‑1 (MQ=255)

                                                                                                                          aaCCATTTTTCAATATC‑ATCTTC‑TGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGCAACAAATGTTAAGTAACTTAATGAAGCTAAATCATGCTTGTTATTAAATACATCGTAAATTCTAAtttt            >  1:272397/1‑139 (MQ=255)

                                                                                                                           aCCATTTTTTATTTTC‑ATTTTC‑TGGATATACACCAGGTACATGTTTAGGTTTGCTTTCATCATCTAACGCAACAAATGTTAAGTAACTTATTGCAGCTAAATCATGTTTTTTCTTCATTACCTCGTCAATTCTAttttta           >  2:150029/1‑138 (MQ=255)

                                                                                                                                 tttCAATATC‑ATCTTC‑TGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGCAACAAATGTTAAGTAACTTAACGCAGCTAAATCATGCTTGTTATTAAATACATCGTCAATTCTAATTTGAACGAcc     <  1:286726/140‑1 (MQ=255)

                                                                                                                                    cAATATC‑ATCTTT‑TGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGCAACAAATGTTAAGTAACTTAATGCAGCTAAATCATGCTTGTTATTAAATACATCGTCAATTCTAATTTGAACGACCACt  <  1:102545/140‑1 (MQ=255)

ACAATCTGTCTTTATATTTTTAGTCTCTAATATGTTGCACTTGAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAACATC‑ATCTTC‑TGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGCAACAAATGTTAAGTAACTTAATGCAGCTAAATCATGCTTGTTATTAAATACATCGTCAATTCTAATTTGAACGACCACT  >  CP000730/2021682‑2021953

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