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 F3 I95 R1 196 14.2 808436 96.0% 776098 85.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP009273 1,659,576 T→C F14S (TTC→TCC)  clcB → voltage‑gated ClC‑type chloride channel ClcB

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,659,5760TC100.0% 65.0 / NA 20F14S (TTC→TCC) clcBvoltage‑gated ClC‑type chloride channel ClcB
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (6/14);  total (6/14)

TTTTGCCGCAAAATAGTCGCCCGTGTTTCATTGCCCATTTCTGCTCATGCATCATCTACACATCTATCCGGATCTGCGCACTATGTTCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCCGTTGCCGGGTTTCGTCATGCGATGCTGCTACTGGAG  >  NZ_CP009273/1659490‑1659661
                                                                                      |                                                                                     
ttttGCCGCAAAATAGTCGCCCGTGTTTCATTGCCCATTTCTGCTCATGCATCATCTACACATCTATCCGGATCTGCGCACTATGTCCCa                                                                                    <  1:141793/90‑1 (MQ=255)
                  gCCCGTGTTTCATTGCCCATTTCTGCTCATGCATCATCTACACATCTATCCGGATCTGCGCACTATGTCCCACCGTCTGCTTATCGCAAc                                                                  <  2:301354/90‑1 (MQ=255)
                      gtgtTTCATTGCCCATTTCTGCTCATGCATCATCTACACATCTATCCGGATCTGCGCACTATGTCCCACCGTCTGCTTATCGCAACAgtc                                                              >  2:161727/1‑90 (MQ=255)
                                gCCCATTTCTGCTCATGCATCATCTACACATCTATCCGGATCTGCGCACTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATtc                                                    >  2:23483/1‑90 (MQ=255)
                                    aTTTCTGCTCATGCATCATCTACACATCTATCCGGATCTGCGCACTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTcgc                                                <  1:33487/90‑1 (MQ=255)
                                     tttCTGCTCATGCATCATCTACACATCTATCCGGATCTGCGCACTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTcgcg                                               <  2:298248/90‑1 (MQ=255)
                                          gCTCATGCATCATCTACACATCTATCCGGATCTGCGCACTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTAt                                                      >  2:280628/1‑78 (MQ=255)
                                          gCTCATGCATCATCTACACATCTATCCGGATCTGCGCACTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTAt                                                      <  1:280628/78‑1 (MQ=255)
                                          gCTCATGCATCATCTACACATCTATCCGGATCTGCGCACTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCtt                                          <  1:57030/90‑1 (MQ=255)
                                                        tACACATCTATCCGGATCTGCGCACTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCCGTTGCCGGGt                            <  2:342254/90‑1 (MQ=255)
                                                         acacATCTATCCGGATCTGCGCACTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCCGTTGCCGGGtt                           >  1:222891/1‑90 (MQ=255)
                                                                      gATCTGCGCACTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTcg                                                 <  2:160586/55‑1 (MQ=255)
                                                                      gATCTGCGCACTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTcg                                                 >  1:160586/1‑55 (MQ=255)
                                                                      gATCTGCGCACTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCCGTTGCCGGGTTTCGTCATGCGAtg              <  1:265061/90‑1 (MQ=255)
                                                                        tCTGCGCACTATGTCCCACCGTCTGTTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCCGTTGCCGGGTTTCGTCATGCGAtgct            <  2:267332/90‑1 (MQ=255)
                                                                        tCTGCGCACTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCCGTTGCCGGGTTTCGTCATGCGAtgct            <  1:270342/90‑1 (MQ=255)
                                                                        tCTGCGCACTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCCGTTGCCGGGTTTCGTCATGCGAtgct            <  2:28698/90‑1 (MQ=255)
                                                                           gcgcACTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCCGTTGCCGGGTTTCGTCATGCGATgctgct         >  1:292310/1‑90 (MQ=255)
                                                                                 tATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCCGTTGCCGGGTTTCGTCATGCGATGCTGCTACTGGa   <  2:222891/90‑1 (MQ=255)
                                                                                  aTGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCCGTTGCCGGGTTTCGTCATGCGATGCTGCTACTGGAg  <  2:173128/90‑1 (MQ=255)
                                                                                      |                                                                                     
TTTTGCCGCAAAATAGTCGCCCGTGTTTCATTGCCCATTTCTGCTCATGCATCATCTACACATCTATCCGGATCTGCGCACTATGTTCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCCGTTGCCGGGTTTCGTCATGCGATGCTGCTACTGGAG  >  NZ_CP009273/1659490‑1659661

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: 

GATK/CNVnator alignment

BRESEQ :: bam2aln output
CGGCTGGCCTCTTTTGCCGCAAAATAGTCGCCCGTGTTTCATTGCCCATTTCTGCTCATGCATCATCTACACATCTATCCGGATCTGCGCACTATGTTCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCCGTTGCCGGGTTTCGTCATGCGATGCTGCTACTGGAGTGGTTGTTCC  >  NZ_CP009273/1659479‑1659671
                                                                                                 |                                                                                               
CGGCTGGCCTCTTTTGCCGCAAAATAGTCGCCCGTGTTTCATTGCCCATTTCTGCTCATGCATCATCTACACATCTATCCGGATCTGCGCACTATGTCCC                                                                                               <  SRR3722235.142904/100‑1 (MQ=60)
           TTTTGCCGCAAAATAGTCGCCCGTGTTTCATTGCCCATTTCTGCTCATGCATCATCTACACATCTATCCGGATCTGCGCACTATGTCCCACCGTCTGCTT                                                                                    <  SRR3722235.143435/100‑1 (MQ=60)
                             gacggcatacgagattgcctcttgtctcgtgggctcggagatgtgtataagagacagGCGCACTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGT                                                                  <  SRR3722235.372314/43‑1 (MQ=60)
                              CCCGTGTTTCATTGCCCATTTCTGCTCATGCATCATCTACACATCTATCCGGATCTGCGCACTATGTTCCACCtgtctcttatacacatctccgagccca                                                                 >  SRR3722235.181747/1‑73 (MQ=60)
                                         agGCCCATTTCTGCTCATGCATCATCTACACATCTATCCGGATCTGCGCACTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCC                                                      <  SRR3722235.284475/98‑1 (MQ=60)
                                               ATTTCTGCTCATGCATCATCTACACATCTATCCGGATCTGCGCACTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCC                                                <  SRR3722235.33856/100‑1 (MQ=60)
                                                     GCTCATGCATCATCTACACATCTATCCGGATCTGCGCACTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCCGTTGCC                                          <  SRR3722235.57667/100‑1 (MQ=60)
                                                          TGCATCATCTACACATCTATCCGGATCTGCGCACTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCCGTTGCCGGGTT                                     >  SRR3722235.225697/1‑100 (MQ=60)
                                                                       CATCTATCCGGATCTGCGCACTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCCtgtctcttatacacatctccgagc                        >  SRR3722235.162431/1‑76 (MQ=60)
                                                                            ATCCGGATCTGCGCACTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCCGTTGCCGGGTTTCGTCATGCGATGCTGCT                   >  SRR3722235.296381/1‑100 (MQ=60)
                                                                                 GATCTGCGCACTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCCGTTGCCGGGTTTCGTCATGCGATGCTGCTACTGG              <  SRR3722235.268596/100‑1 (MQ=60)
                                                                                   TCTGCGCACTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCCGTTGCCGGGTTTCGTCATGCGATGCTGCTACTGGAG            <  SRR3722235.273990/100‑1 (MQ=60)
                                                                                             ATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCCGTTGCCGGGTTTCGTCATGCGATGCTGCTACTGGAGTGGTTGTTCC  >  SRR3722235.66720/1‑100 (MQ=60)
                                                                                             ATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCCGTTGCCGGGTTTCGTCATGCGATGCTGCTACTGGAGTGGTTGTTCC  >  SRR3722235.83616/1‑100 (MQ=60)
                                                                                                 |                                                                                               
CGGCTGGCCTCTTTTGCCGCAAAATAGTCGCCCGTGTTTCATTGCCCATTTCTGCTCATGCATCATCTACACATCTATCCGGATCTGCGCACTATGTTCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCCGTTGCCGGGTTTCGTCATGCGATGCTGCTACTGGAGTGGTTGTTCC  >  NZ_CP009273/1659479‑1659671

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: