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 F13 I0 R1	91	33.2	766976	92.9%	712520	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,232,465	G→C	100%	A124P (GCG→CCG)	USA300HOU_1157 →	non‑specific serine/threonine protein kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,232,465	0	G	C	100.0%	110.9 / ‑6.5	34	A124P (GCG→CCG)	USA300HOU_1157	non‑specific serine/threonine protein kinase
Reads supporting (aligned to +/- strand): ref base G (0/0); major base C (10/23); minor base A (0/1); total (10/24)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

AAGAAGATGACTGTTACTACTTAGTAATGGAATATATCGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATGCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTAAAGCTTTAAGTGAGACGTCTTTAACTCAGACTAATCATGTG  >  CP000730/1232328‑1232602

aagaagAGGACTGTTACTACTTAGGAATGGAATATATCGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATccgc                                                                                                                                        <  1:127737/141‑1 (MQ=255)

  gaagaTGACTGTTACTACTTAGTAATGGAATATATCGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCAt                                                                                                                                      <  2:127571/141‑1 (MQ=255)

  gaagaTGACTGTAACTACTTAGTAATGAAAAATATCGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCAt                                                                                                                                      <  1:137859/141‑1 (MQ=255)

        taCTGTTACTACTTAGTAATGGAATATATCGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATg                                                                                                                                <  1:328526/140‑1 (MQ=255)

        gACCGTTACTATGTAGTAATGGAATATATCGAAGGCCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATg                                                                                                                                <  2:107543/141‑1 (MQ=255)

         aCTGTTACTACTTAGTAATGGAATATATCGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGc                                                                                                                               <  1:2591/141‑1 (MQ=255)

         aCTGGTACTACTTAGTAATGGAATATATCGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGc                                                                                                                               <  2:72680/141‑1 (MQ=255)

          cTGTTACTACTTAGTAATGGAATATATCGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGACTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCg                                                                                                                              <  2:270858/141‑1 (MQ=255)

                ctactTAGTAATGGAATATATCGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGt                                                                                                                        <  2:237293/141‑1 (MQ=255)

                ctactTAGTAATGGAATATATCGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCAGGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCGTGATATGCGTATTGt                                                                                                                        <  2:108988/141‑1 (MQ=255)

                 tacgTAGTAATGGAATATATCGAAGGTCCGACTGTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTa                                                                                                                       <  2:222260/141‑1 (MQ=255)

                          aTGGAATATATCGAAGGACCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGat                                                                                                              <  1:227712/141‑1 (MQ=255)

                                                cTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTaa                                                                                        >  2:242964/1‑141 (MQ=255)

                                                               ttGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATaaaa                                                                         >  2:237677/1‑141 (MQ=255)

                                                               ttGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATaaaa                                                                         >  2:131117/1‑141 (MQ=255)

                                                                              cATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTg                                                          <  2:5057/141‑1 (MQ=255)

                                                                                   agggtagagactgCGAATAATTTAACGAATCAAATATTGGATGGCATTAAACATCAGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGAtttt                                                     <  2:74011/129‑1 (MQ=255)

                                                                                   aGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGAtttt                                                     <  2:352908/141‑1 (MQ=255)

                                                                                   aGTGTGGAAAAAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGACACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGAtttt                                                     <  2:288882/141‑1 (MQ=255)

                                                                                     tgtTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTGGATTTTgg                                                   >  1:238055/1‑141 (MQ=255)

                                                                                     tgtTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAAAATTTGATTTTgg                                                   >  1:55131/1‑141 (MQ=255)

                                                                                         gACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAAtt                                               <  1:81870/141‑1 (MQ=255)

                                                                                              aGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTaa                                          >  2:61412/1‑141 (MQ=255)

                                                                                                    tAAGTTTACGAATCAAATTTTGGATGGAATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTAAAGCgtt                                    <  2:192989/141‑1 (MQ=255)

                                                                                                      aTTTTAAGAATCAAATAATGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGAGATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTAAAGCTTTaa                                  <  1:307592/141‑1 (MQ=255)

                                                                                                          taagAAACAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTAAAGCTTTAAGtta                              <  2:81795/138‑3 (MQ=255)

                                                                                                          tACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTAAAGCTTTAAGTga                              <  1:225452/141‑1 (MQ=255)

                                                                                                                  aaaTATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTAAAGCTTTAAGTGAGACGTCtt                      <  1:129521/141‑1 (MQ=255)

                                                                                                                  aaaTATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGAAATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTAAAGCTTTAAGTGAGACGTCtt                      <  1:39582/141‑1 (MQ=255)

                                                                                                                  aaaTAGTGGATGGCATTAAACATACGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTAAAGCTTTAAGTGAGACGTCtt                      <  2:300893/141‑1 (MQ=255)

                                                                                                                         ggATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTAAAGCTTTAAGTGAGACGTCTTTAACTCa               >  2:375685/1‑141 (MQ=255)

                                                                                                                         ggATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTAAAGCTTTAAGGGAGACGTCTTTAACTCa               >  2:1907/1‑141 (MQ=255)

                                                                                                                                   aaaCATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTAAAGCTTTAAGTGAGACGTCTTTAACTCAGACTAATCAt     >  2:252511/1‑141 (MQ=255)

                                                                                                                                   aaaCATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTAAAGCTTTAAGTGAGACGTCTTTAACTCAGACTAATCAt     >  2:182285/1‑141 (MQ=255)

                                                                                                                                      cATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTAAAGCTTTAAGTGCGACGTCTTTAACTCAGACTAATCAtgtg  <  1:242964/141‑1 (MQ=255)

AAGAAGATGACTGTTACTACTTAGTAATGGAATATATCGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATGCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTAAAGCTTTAAGTGAGACGTCTTTAACTCAGACTAATCATGTG  >  CP000730/1232328‑1232602

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